Molecular conformations

In this Masters thesis computational modelling techniques were employed to investigate iron-free apo-Lactoferrin (apo-Lf) structural conformation changes in the presence of variant temperature and pH. These conditions represent the environment most milk protein goes through in food processing and the production of food products.

162p runthenight04 02-02-2023 8 3   Download

The exocyclic hydroxymethyl group of the
-D-1-amino-1-deoxyglucopyranose can rotate around the carbon-carbon bond. Potential energy surface for this rotation has been investigated using ab initio quantum chemical methods. Relevant stationary points, including for the first time rotational transition states have been characterized by full geometry optimization using basis sets 6-31G(d) and 6-31G(2d,lp). There is a total of six stationary points along the hydroxymethyl rotational surface, including three minima and three transition states were identified.

5p uocvong04 24-09-2015 42 2   Download

Departamento de Bioquı´mica y Biologı´a Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Spain; Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA Reduction potential determinations of K75E, E139K and E301A ferredoxin-NADP+ reductases provide valuable information concerning the factors that contribute to tune the flavin reduction potential. Thus, while E139 is not involved in such modulation, the K75 side-chain tunes the flavin potential by creating a defined environment that modulates the FAD conformation. ...

6p system191 01-06-2013 34 4   Download

Vibrio choleraehemolysin (HlyA), a water-soluble protein with a native monomeric relative molecular mass of 65 000, forms transmembrane pentameric channels in target bio-membranes.TheHlyAbinds to lipid vesicles nonspecifically and without saturation; however, self-assembly is triggered specifically by cholesterol.Here we show that the HlyA partitioned quantitatively to amphiphilic media irrespective of their compositions, indicating that the toxin had an amphiphilic surface.

8p research12 23-04-2013 56 4   Download

Glutamate decarboxylase is a pyridoxal 5¢-phosphate-dependent enzyme responsible for the irreversiblea-decar-boxylation of glutamate to yield 4-aminobutyrate. In Escherichia coli, as well as in other pathogenic and non-pathogenic enteric bacteria, this enzyme is a structural component of the glutamate-based acid resistance system responsible for cell survival in extremely acidic conditions (pH

8p tumor12 22-04-2013 30 3   Download

Ascorbic acid is often regarded as an antioxidantin vivo, where it protects against cancer by scavenging DNA-dam-aging reactive oxygen species. However, the detailed mech-anism of the action of ascorbic acid on genetic DNA is still unclear. We examined the effect of ascorbic acid on the higher-order structure of DNA through real-time observa-tion by fluorescence microscopy. We found that ascorbic acid generates a pearling structure in single giant DNA molecules, with elongated and compact regions coexisting along a molecular chain. ...

6p tumor12 20-04-2013 32 5   Download

The catalytic activity of phenylalanine hydroxylase (PAH, phenylalanine 4-monooxygenase EC 1.14.16.1) is regulated by three main mechanisms, i.e. substrate (L-phenylalanine, L-Phe) activation, pterin cofactor inhibition and phos-phorylation of a single serine (Ser16) residue.To address the molecular basis for the inhibition by the natural cofactor (6R)-L-erythro-5,6,7,8-tetrahydrobiopterin, its effects on the recombinant tetrameric human enzyme (wt-hPAH) was studied using three different conformational probes, i.e.

10p tumor12 20-04-2013 34 3   Download

Molecular mechanics calculations on conformers of Ac-HGly-NHMe, Ac-b 2 -HAla-NHMe and Ac-b 3 -HAla-NHMe indicate that low-energy conformations of the b-amino acids backbone, corresponding to gauche rotamers around the Ca–Cbbond, may overlap canonical backbone conformers observed for a-amino acids. Therefore, Sub-stance P (SP) was used as a model peptide to analyse the structural and biological consequences of the substitution of Phe7andPhe8by(R)-b 2 -HPheandofGly9byHGly (R)-b 2 -HAla or (S)-b 3 -HAla....

11p tumor12 20-04-2013 33 3   Download

To investigate the structural function of the C-terminal amide group of endomorphin-2 (EM2, H-Tyr-Pro-Phe-Phe-NH2), an endogenous l-opioid receptor ligand, the solution conformations of EM2 and its C-terminal free acid (EM2OH, H-Tyr-Pro-Phe-Phe-OH) in TFE (trifluoroethanol), water (pH 2.7 and 5.2), and aqueous DPC (dodecylphosphocholine) micelles (pH 3.5 and 5.2) were investigated by the combination of 2D 1 H-NMR meas-urement and molecular modelling calculation.

19p fptmusic 12-04-2013 32 4   Download

Retinol-binding protein transports retinol, and circulates in the plasma as a macromolecular complex with the protein transthyretin. Under acidic con-ditions retinol-binding protein undergoes a transition to the molten globule state, and releases the bound retinol ligand. A biased molecular dynamics simulation method has been used to generate models for the ensemble of conformers populated within this molten globule state.

13p fptmusic 12-04-2013 39 3   Download

Defining how the agonist–receptor interaction differs from that of the antagonist–receptor and understanding the mechanisms of receptor activation are fundamental issues in cell signalling. The V1a vasopressin receptor (V1aR) is a member of a family of related G-protein coupled receptors that are activated by neurohypophysial peptide hormones, including vasopressin (AVP). It has recently been reported that anarginyl in the distalN-terminus of theV1a Riscritical for binding agonists but not antagonists....

8p fptmusic 12-04-2013 28 2   Download

In a previous study we showed that natural polyamines interact in the nuclear environment with phosphate groups to form molecular aggregates [nuclear aggregates of polyamines (NAPs)] with estimated molecular mass values of 8000, 4800 and 1000 Da. NAPs were found to interact with genomic DNA, influence its conformation and interfere with the action of nucleases.

11p fptmusic 11-04-2013 43 2   Download

Small heat shock proteins (sHSPs) function as molecular chaperones, pre-venting stress induced aggregation of partially denatured proteins and pro-moting their return to native conformations when favorable conditions pertain. Sequence similarity between sHSPs resides predominately in an internal stretch of residues termed the a-crystallin domain, a region usually flanked by two extensions.

15p awards 06-04-2013 37 3   Download

The gene encoding a threonine dehydrogenase (TDH) has been identified in the hyperthermophilic archaeon Pyrococcus furiosus. The Pf-TDH pro-tein has been functionally produced in Escherichia coliand purified to homogeneity. The enzyme has a tetrameric conformation with a molecular mass of
155 kDa.

8p dell39 27-03-2013 26 3   Download

The catalytic competence of the natural thrombin mutant with deletion of the Lys9 residue in the A-chain (DK9) was found to be severely impaired, most likely due to modification of the 60-loop conformation and catalytic triad geometry, as supported by long molecular dynamics (MD) simula-tions in explicit water solvent.

11p dell39 27-03-2013 37 4   Download

The functional activities of proteins are closely related to their molecular structure and understanding their structure–function relationships remains one of the intriguing problems of molecular biology. We investigated struc-tural changes in 17b-hydroxysteroid dehydrogenase from the fungus Cochliobolus lunatus(17b-HSDcl) induced by pH, temperature, salt, urea, guanidine hydrochloride, and coenzyme NADPH binding.

11p inspiron33 25-03-2013 41 4   Download

We solved the crystal structure ofStreptococcus agalactiaeserine⁄threonine phosphatase (SaSTP) using a combination of single-wavelength anomalous dispersion phasing and molecular replacement. The overall structure resem-bles that of previously characterized members of the PPM⁄PP2C STP fam-ily.

10p galaxyss3 19-03-2013 28 2   Download

A key molecular event in prion diseases is the conversion of the cellular conformation of the prion protein (PrP C ) to an altered disease-associated form, generally denoted as scrapie isoform (PrP Sc ). The molecular details of this conformational transition are not fully understood, but it has been suggested that an intermediate on the folding pathway of PrP C may be recruited to form PrP Sc .

13p media19 06-03-2013 39 3   Download

Micro-myoglobin, the isolated heme-binding subdomain of myoglobin, is a valuable model system for the investigation of heme recognition and bind-ing by proteins, and provides an example of protein folding induced by co-factor binding.

8p media19 05-03-2013 42 3   Download

The oligomeric state and kinetics of ligand binding were measured for wild-type cytoglobin. Cytoglobin has the classical globin fold, with an extension at each extremity of about 20 residues. The extended length of cytoglobin leads to an ambiguous interpretation of its oligomeric state.

9p mobifone23 21-01-2013 49 4   Download