Modelling the substitutability

In this thesis, using the data from the Viral Genome Resource at National Center for Biotechnology Informa-tion (NCBI), we propose the ROTA model that has been specifically estimated formodeling the evolution of rotavirus.

56p tamynhan0 04-07-2020 18 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

The activity of the digestiveb-glycosidase fromSpodoptera frugiperda (Sfbgly50, pH optimum 6.2) depends on E399 (pKa¼4.9; catalytic nucleophile) and E187 (pKa¼7.5; catalytic proton donor). Homology modelling of the Sfbgly50 active site confirms that R97 and Y331 form hydrogen bonds with E399. Site-directed mutagenesis showed that the substitution of R97 bymethionine or lysine increased the E399 pKa by 0.6 or 0.8 units, respectively, shifting the pH optima of these mutants to 6.5.

10p fptmusic 12-04-2013 35 3   Download

Integrase (IN) is the retroviral enzyme responsible for the integration of the DNA copy of the retroviral genome into the host cellDNA. TheC-terminal domainof INis involved in DNA binding and enzyme multimerization. We previ-ously performed single amino acid substitutions in the C-terminal domain of the avian leukemia and sarcoma vir-uses (ALSV) IN [Moreauet al. (2002). Arch. Virol.147, 1761–1778].

13p fptmusic 12-04-2013 42 4   Download

Staphylococcalnuclease is a single domain protein with 149 amino acids. It has no disulfide bonds, which makes it a simple model for the study of pro-tein folding. In this study, 20 mutants of this protein were generated each with a single base substitution of glycine for negatively charged glutamic acid or aspartic acid. Using differential scanning microcalorimetry in ther-mal denaturation experiments, we identified two mutants, E75G and E129G, having approximately 43% and 44%, respectively, lowerDHcal values than the wild-type protein....

8p fptmusic 11-04-2013 44 3   Download

Staphylococcal nuclease (SNase) is a model protein that contains one domain and no disulfide bonds. Its stability in the native state may be maintained mainly by key amino acids. In this study, two point-mutated proteins each with a single base substitution [alanine for tryptophan (W140A) and alanine for lysine (K133A)] and two truncated fragment proteins {positions 1–139 [SNase(1–139) or W140O] and positions 1–141 [SNase(1–141) or E142O]} were generated.

7p fptmusic 11-04-2013 39 3   Download

The substrate specificity of the nuclear inclusion protein a (NIa) proteolytic enzymes from two potyviruses, the tobacco etch virus (TEV) and tobacco vein mottling virus (TVMV), was compared using oligopeptide substrates. Mutations were introduced into TEV protease in an effort to identify key determinants of substrate specificity. The specificity of the mutant enzymes was assessed by using peptides with complementary substitutions. The crys-tal structure of TEV protease and a homology model of TVMV protease were used to interpret the kinetic data....

0p awards 05-04-2013 36 2   Download

Substitution oftrans-proline at three positions in ubiquitin (residues 19, 37 and 38) produces significant context-dependent effects on protein stability (both stabilizing and destabilizing) that reflect changes to a combination of parameters including backbone flexibility, hydrophobic interactions, solvent accessibility to polar groups and intrinsic backbone conformational preferences. Kinetic analysis of thewild-type yeast protein reveals a predominant fast-folding phase which conforms to an apparent two-state folding model. ...

11p awards 05-04-2013 49 4   Download

Models for the binding of the sarcin–ricin loop (SRL) of 28S ribosomal RNA to ricinAchain (RTA) suggest that several surface exposed arginine residues surrounding the active site cleft make important interactions with the RNA substrate. The data presented in this study suggest differing roles for these arginyl residues. Substitution of Arg48 or Arg213with Ala lowered the activity of RTA 10-fold. Furthermore, substitutionofArg213withAsp lowered theactivityofRTA 100-fold.

10p dell39 03-04-2013 37 4   Download

The role of the two disulfide bonds (Cys4–Cys60 and Cys18–Cys29) in the activity and stability of goose-type (G-type) lysozyme was investigated using ostrich egg-white lysozyme as a model. Each of the two disulfide bonds was deleted separately or simultaneously by substituting both Cys residues with either Ser or Ala.

13p media19 06-03-2013 33 3   Download