While R256T and K364R are at different positions, both mutations are present in the active site. Researchers were unable to get kinetics data on R256T. What does this tell you about its ability to function properly? Why might K364R be tolerated better than R256T?
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- Replacing Glu-165 with alanine has the most significant impact on the catalytic activity of all the mutations examined. Does this observation agree with your predictions about the roles of the various active site residues, informed by the computational mutagenesis?The objective is to study a novel protease P isolated from the digestive tract of an Amazonian insect. This protease can exist into two forms Pi and Pa which have identical amino acid sequences (both of 80 kDa). However, only Pa shows proteolytic activity. To better understand the activation mode of Pi (inactive form) in Pa (active form), the following experiment was done using DIPF. DIPF (diisopropylphosphofluoridate) is a well-known irreversible inhibitor of serine proteases. It reacts with the catalytic serine residue of the active site of proteases as shown below: Enzyme -CH₂OH + CH(CH3)2 O F-P=0 O CH(CH3)2 Diisopropylphospho- fluoridate (DIPF) Enzyme -CH,—O CH(CH3)2 O <=0 O CH(CH3)2 DIP-Enzyme Both proteases Pa and P₁ were incubated with 32P-DIPF for 30 min at 37°C, and then dialysed to remove excess of unreacted radiolabelled reagent. The two proteases were then analyzed in Sodium Dodecyl Sulphate-Polyacrylamide Gel Electrophoresis (SDS-PAGE), with and without 2-mercaptoethanol.…In the "biochemical assay of b-galactosidase activity", what is o-nitrophenyl-b-D-galactosidase (ONPG) used for? O When ONPG is cleaved by b-galactosidase, we are able to assay b-galactosidase activity. O It provides essential nutrients for bacterial growth. It partially disrupts the cell membrane to allow cellular proteins to diffuse out of the cell. O ONPG cleaves the b-galactosidase that is made by the lac operon so we can see how much activity there is in the cell. ONPG cleaves galactose so we can measure how much lactose there is in the cell.
- Mutational analysis of the important amino acids in the catalytic triad of serine proteases showed that replacing Asp102 or modifying His57 with amethyl group decreased the reaction rate about 5000-fold. However,mutating Ser195 decreased the reaction rate a millionfold. Discuss why mutating Ser had a larger impact than the other members of the catalytic triad.In each of the following cases, predict whether the pKa value of the first residue will be upshifted or downshifted relative to the typical pKa value (Table 2.1) based on the microenvironment. Briefly (in no more than 2-3 sentences) explain your reasoning. (a) A His residue adjacent to two Arg residues on the surface of a protein(b) A Cys residue adjacent to an Asp residue in the active site of an enzyme(c) A Lys residue buried in the hydrophobic core of a globular proteinA classic way to isolate thymidylate synthase–negative mutants of bacteriais to treat a growing culture with thymidine and trimethoprim. Most ofthe cells are killed, and the survivors are greatly enriched in thymidylatesynthase–negative mutants.(a) What phenotype would allow you to identify these mutants?(b) What is the biochemical rationale for the selection? (That is, why are themutants not killed under these conditions?)(c) How would the procedure need to be modified to select mammalian cellmutants defective in thymidylate synthase?
- (c) On the right is a diagram of the ac tive site of E. coli aspartate aminotrans- ferase illustrating the cofactor pyridoxal phosphate (labeled PLP) with the dicar- boxylic acid maleate (labeled MAL) bound in the active site. The structural formula of maleate is shown on the right. Am 194 MAL Arg292 Arg386 Ilx17 Lauf 'coo- H get H Coo- Maleate (c1) Draw the structure of L-aspartate and draw a border around the atoms in the amino acid that maleate simulates. (c2) Identify the active site residues that make hydrogen bonds and electrostatic interac- tions with the oxygen atoms of the carboxylate groups of maleate in the diagram above. Identify the carboxylate groups according to the numbering in the diagram of maleate above. Indicate the hydrogen donor groups of the active site residues. (C3) Compare and draw the structures of L-Arg and L-Lys. On the basis of the diagram why does replacement of an arginine for a lysine have an effect on substrate binding to AspAT? (c4) Of the mutant…Catalytic residues are often found in loops between helices or strands for increased mobility duringcatalysis. Is the catalytic Cys predicted to be located in a loop between helices/strands?Are the other two catalytic residues, His and Asn, also found in loops?In Figure 12-26, provide a biochemical mechanism forwhy HP-1 can bind to the DNA only on the left side of thebarrier insulator. Similarly, why can HMTase bind onlyto the DNA on the left of the barrier insulator?
- We learned that three different amino acid transformations of PLP-dependent enzymes canresult from different conformations of the PLP-amino acid imine adduct in the active site.Starting from the PLP adduct of (S)-serine, show mechanisms fora) Decarboxylation of serineb) Racemization of serinec) Conversion of serine to glycine and formaldehyde.In site-directed mutagenesis experiments of an enzyme, scientists altered an aspartate residue to glutamate, lysine, phenylalanine, or valine. Which substitution is expected to have the least effect on enzymatic acitivity? Group of answer choices Glutamate Valine Lysine PhenylalanineCTP synthetase catalyzes the glutamine-dependent conversion of UTP to CTP. The enzyme is allosterically inhibited by the product, CTP. Mammalian cells defective in this allosteric inhibition are found to have a complex phenotype: They require thymidine in the growth medium, they have unbalanced nucleotide pools, and they have an elevated spontaneous mutation rate. Explain the likely basis for these observations.