3CLpro is a cysteine protease, which are among the most common proteases in biochemistry, however they are a structurally diverse family of enzymes especially in the organization of the active site amino acids. A group of scientists have reported a potential drug molecule based on a binding study using circular dichroism. They report that the molecule binds to the active site. Can the experiment support the claims, why or why not? Which techniques might be used to support this claim?
Q: The amino acid glycine is often used as the main ingredient of a buffer in biochemical experiments.…
A: Every biological process is pH-dependent, which means that a slight change in pH results in a…
Q: enzymatic activity. Which of the following procedures might help you to obtain soluble,…
A: Introduction: Genetically modified organisms are those in which genetic engineering techniques are…
Q: There are two competing processes for the manufacture of lactic acid, chemical and biochemical…
A: Lactic acid is an organic compound, its Chemical name is 2-hydroxypropanoic acid and belongs to…
Q: A biochemist is trying to determine the type of proteases they have isolated from walrus blubber.…
A: Enzymes are highly specialized proteins that have extraordinary catalytic power, greater than that…
Q: Radioactive uracil can be used to label all of the pyrimidine residues inDNA. Using either names or…
A: Allosteric regulation is the regulation of an enzyme by binding an effector molecule at a site other…
Q: From a medicinal chemistry (and a pharmacologist) perspective, functional groups provide specific…
A: Pharmacokinetics defines the fate of a drug in the body. It includes absorption, distribution,…
Q: Protease is an enzyme that catalyzes the breaking of amide bonds which is very stable at “mild”…
A: The reaction mechanism which follows general acid-base catalysis is as follows.:
Q: complete the following mechanism showing the cleavge of the peptide bond for the following cysteine…
A: ghhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhf vcxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Q: An active site of a hypothetical serine protease with a peptide substrate bound is shown below:…
A: Serine peptidases are enzymes that are mainly concerned with the cleaving of the peptide bonds in…
Q: TFQFPFAEQL EKVAEQFPTF QILNEEGEVV NEEAMPELSD EOLKELMRRM : (amino h (amino) (amino i (amino amg…
A: These six amino acid residues are split between two subunits. Together, they form a BASIC tunnel…
Q: Saccharide X, a sugar composed of repeating cellobiose and maltose, is a constituent of two…
A: Glycoproteins are consisted of protein and glycan moiety which is involved in several biological…
Q: Serine Proteases, such as chymotrypsin, contain Ser/Asp/His as a catalytic triad (i.e. three…
A: Enzymes are a class of proteins except for ribozymes (class of RNA) that enhance the rate of…
Q: The active site of lysozyme contains two amino acid residues essential for catalysis: Glu35 and…
A: Lysozyme is an antibacterial enzyme that plays a crucial role in prevention of bacterial infections.…
Q: 1 Specify the role each of the following amino acids play within the crystal structure and/or active…
A: "Since you have asked multiple questions, we will solve the first question for you. If you want a…
Q: The enzyme lysozyme hydrolyzes glycosidic bonds in peptidoglycan, an oligosaccharide found ir…
A: Enzymes are the biocatalysts that are specific for the substrate binding to carry out all the…
Q: Acetylating agents such as acetic anhydride react preferentially with primaryamines, iodoacetate…
A: Acetic anhydride or ethanoic anhydride, is the chemical compound. It is the simplest isolable…
Q: Ethyl alcohol is sometimes used in hospital emergency rooms to treat patients who have ingested…
A: The main components of the antifreeze are methanol, glycerol, ethylene glycol, and propylene glycol.…
Q: A biochemist is trying to determine the type of proteases they have isolated from walrus blubber.…
A: The modification of amino acid side chains using amino acid specific covalent labeling is an…
Q: Bovine chymotrypsin is a serine protease. The enzyme is structurally stable over the pH range of…
A: Chymotrypsinogen enzyme is responsible for the activation of trypsinogen into trypsin during the…
Q: BIM-46187 is a protein inhibitor that binds to the a-subunit of the G. protein. It prevents the…
A: Cell signaling is the conversion of the information in a signal into cellular response. Ligands,…
Q: When specific conditions are met, the creation of peptide bonds rather than the hydrolysis of…
A: Proteins are unbranched polymers constructed from 20 standard α-amino acids. They have four levels…
Q: Phosphatidylserine (PS) is considered to be an intermediate in the biosynthesis of…
A: Phosphatidylserine is a lipid molecule that is negatively charged. It is composed of a backbone of…
Q: L-Amino-acid oxidase will catalyze reactions of L-amino acids but not of D-amino acids. Which of the…
A: Since you have asked multiple questions, we will answer only first question for you. In order to get…
Q: A mutation results in the change of Ser to Asp in the active site of chymotrypsin. Most likely, the…
A: >serine protease Catalyzes the hydrolysis of peptide bonds, on the carboxyl side of bulky…
Q: A biochemist is trying to determine the type of proteases they have isolated from walrus blubber.…
A: Hi! Thank you for the question. We are authorized to answer one question at a time, since you have…
Q: Globular proteins with multiple disulfide bonds must be heated longer and at higher temperature to…
A: Bovine pancreatic trypsin inhibitor is a small protein with a very small hydrophobic core. This…
Q: The following data describe the catalysis of cleavage of peptide bonds in small peptides by the…
A: Peptide bond cleavage is the basic process of hydrolysis of a polypeptide where the peptide bond…
Q: A seven-residue peptide was found to have an amino acid composition including glu, val, Lys, met,…
A: phenyl thiohydantoin (PTH)- amino acid derivative The sequence of amino acid for heptapeptide…
Q: Please draw the arrow-pushing mechanism to create the polyketide backbone chain of TYLOSIN. If two…
A: Streptomycetes, a type of soil bacterium, create the majority of polyketides, an important class of…
Q: During successful purification of every enzyme, the following may be expected: Select ALL that…
A: Enzyme purification and characterization is of great importance in obtaining information about…
Q: The enzymatic activity of lysozyme is optimal at pH 5.2 and decreases above and below this pH value.…
A: The enzyme lysozyme cleaves the glycosidic bond that connects N-acetyl muramic acid with the N-…
Q: Phosphoproteins are formed when a phosphate group is esterified to an -OH group of a Ser, Thr, or…
A: Phosphoproteins are the conjugated proteins that are post-translationally modified by the attachment…
Q: The following data describe the catalysis of cleavage of peptide bonds in small peptides by the…
A: The enzymes that cleave the peptide bonds are known as proteases. There are many types of proteases…
Q: Xylose racemase is a bacterial enzyme that converts the sugar D-xylose to L-xylose, which is needed…
A: Pka of amino acids in the active site changes according to the surrounding environment. Pka increase…
Q: 10. Chymotrypsin is a serine protease enzyme. The Km for the reaction of chymotrypsin with…
A: a. Serine present in the active site is a nucleophile here and it gets activated by proton…
Q: What is the first thing that must occur in order for the catalysis of the peptide bond to begin.…
A: Macromolecules are large organic molecules composed of thousands of covalently connected atoms and…
Q: The bioactive conformation of lead compound I was confirmed when a crystal structure was r. obtained…
A: The amino acids present in the active sites of an enzyme are responsible for the specificity of the…
Q: RuBP carboxylase is by no means an ideal enzyme. Describe some of the problems with its active site…
A: Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyses the inorganic CO2 incorporation…
Q: The diagram below shows the substrate binding cleft for a protease, providing the substrate…
A: Proteases are enzymes which digest the proteins by cleaving the peptide bonds at specific locations.…
Q: . Radioactive uracil can be used to label all of the pyrimidine residues in DNA. Using either names…
A: When the radioactive adenine, particularly uracil, was used as the precursors, highly labeled DNA…
Q: . Phosphatidylserine (PS) is considered to be an intermediate in the biosynthesis of…
A: Phosphatidylserine : It is fatty substance produced in the body that covers and protects every cell…
Q: The enzyme mutase which is important for the synthetic of tyrosine and phenylalanine in…
A: 2.The Curve showing the kinetics of chorismate would shift to the right.
Q: explain why A liposome of 1;1 molar ratio of cholesterol to phospholipids will be the optimum…
A: Liposomes are artificially engineered vesicles for drug transport. There membranes are composed of 2…
Q: 7. Chalcone isomerase catalyzes the reaction illustrated below. A series of modification experiments…
A: Chalcone isomerase is an enzyme in Flavonoid pathway of Anthocyanine biosynthesis and catalyze the…
Q: Which of the following drugs is a less potent microsomal triglyceride transfer protein (MTP)…
A: The half maximal inhibitory concentration or IC50 value is a measure of the potency of a substance…
Q: Radioactive uracil can be used to label all of the pyrimidine residues in DNA. Using either names or…
A: The nucleotides are classified as purines and pyrimidine. The purines are adenine and guanine. The…
Q: A decapeptide which could resist burns was isolated from an endemic plant from Mt. Mayon. Deduce the…
A: The cleavage sites of the different enzymes and chemical compounds used for the determination of the…
Q: "Potassium Bromate (KBr03) is added to flour as a softener that strengthens the texture of bread. It…
A: Disulfide bonds are covalent bonds which forms between the side chain thiol groups of cysteine…
Q: An enzyme contains an active site aspartic acid with a pKa = 5.0, whichacts as a general acid…
A: Enzymes contain ionizable groups at the active site for general acid catalysis. The activity of the…
3CLpro is a cysteine protease, which are among the most common proteases in biochemistry, however they are a structurally diverse family of enzymes especially in the organization of the active site amino acids. A group of scientists have reported a potential drug molecule based on a binding study using circular dichroism. They report that the molecule binds to the active site. Can the experiment support the claims, why or why not? Which techniques might be used to support this claim?
Trending now
This is a popular solution!
Step by step
Solved in 3 steps
- Small molecules are used as inhibitors of protein action - as drugs. They most often do this by blocking the active site within the protein. Potential drugs can be screened computationally to determine if they are strongly bound to the protein. Figure 1 shows a possible conformation of a candidate drug molecule, 4-bromo-2- carboxymethylamide-pyrrole (abbreviation: BCMAP) at the active site of a protein (abbreviation: PR). Figure 2 shows the full protein structure whilst figure 3 shows a known inhibitor of the protein at the site, overlayed with another calculated conformer of BCMAP. (a) Explain what types of interactions, both intermolecular and intramolecular, that a molecular mechanics forcefield must be able to describe in order to be able to accurately determine the geometry of BCMAP in the protein. Identify which interactions will be the most important to describe accurately. Figure 1.4-bromo-2-carboxymethylamide-pyrrole (BCMAP) (C, N, O, and Br atoms in yellow, blue, red, and…An active site of a hypothetical serine protease with a peptide substrate bound is shown below: This serine protease has 3 specificity pockets (S1, S2, S1') as shown in the figure above. S1 pocket has a glutamic acid in the bottom, the S2 pocket is small and hydrophobic, and the S1' pocket is deep and hydrophobic. Based on this information you can conclude that R1 is most likely side chain of a. Asp b. Lys c. Lle d. Gly e. Pheif the reaction pH drops significantly (pH=2 for example), how would reaction catalyzed be serine proteases be affected? why? (assumin that the rest of the protein structure remain intact)
- The Commercial Trainee Program of the Pharma Biotec Industry, opened selection to admit candidates who would help in the development of a more efficient production protocol of Ibuprofen, a non-colloidal anti-inflammatory. Basically, the challenge stimulated obtaining high enantiomeric purity of the final product. In this way, the candidates proposed the use of immobilized enzymes for the process. Tick the most coherent alternative to justify the choice of using immobilized enzymes by the candidates for the case mentioned above in the question. (Only one statement is true)* A)The use of immobilized enzymes was an interesting strategy, since different immobilization techniques can be used, such as adsorption and covalent. b) The use of immobilized enzymes was consistent since the immobilization process can further favor the regioselectivity , enantioselectivity and stereoselectivity properties of the enzymes, which will favor the enantiomeric purity of the drug. c) The use of…1 ).Which of the following accurately describes substrate specificity for serine proteases? A.The binding cleft B.Mg2+ metal activated enzyme C.The catalytic triad D.Facilitates redox chemistry E.Stabilizes the transition state 2). Which of the following amino acid residues would not provide a side chain for acid-base catalysis at physiological pH? select all that apply leucine aspartic acid histidine lysine Please answer both correct i will give u upvote.Shown below is a substrate for a Trypsin. Draw the mechanism for this serine protease using the artificial substrate. Be sure to draw the catalytic triad, and show the role of the oxyanion hole. Draw the complete structure of every intermediate and product and PUSH ARROWS!!!!! Do not abbreviate structures using R and R' H₂N _N_CH. сно CH₂ CH₂ CH₂ NH d=19H₂ NH₂ O CH- H₂C HN O CH
- The oxyanion hole of a serine protease has which of the following roles (select all correct answers)? Question 3 options: Acid-base catalysis Proximity and orientation effects Transition state stabilization Induced fitThe diagram below shows the substrate binding cleft for a protease, providing the substrate structure, and indicating the residues (using one-letter code) that line the four specificity pockets. 1 M F H₂N K R IZ 2 3 P F S W оо E 4 The protease is known to cleave the amide linkage between W and E residues for substrates containing the WEFD sequence. Using 3-letter code with amino acids linked by a "dash" (ex. GLY-ALA), the N-terminal product is A and the C-terminal product is AWhen performing his experiments on protein refolding, Christian Anfinsen obtained a quite different result when reduced ribonuclease was reoxidized while it was still in 8 M urea and the preparation was then dialyzed to remove the urea. Ribonuclease reoxidized in this way had only 1% of the enzymatic activity of the native protein. Why were the outcomes so different when reduced ribonuclease was reoxidized in the presence and absence of urea?
- Some of the following four amino acids : alanine, arginine, histidine, aspartic acid would provide a side chain for acid-base catalysis at physiological pH (assume pK of each amino acid is equal to pK value for the free amino acid in solution). Explain for each amino acid how and why each would or would not provide the side chain residue to support acid-base catalysis at physiological pH.Data from enzyme inhibition are used to determine a Kmapp and Vmax PP. Comparison of these values with assays run without inhibitor are used to understand how the inhibition is occurring. This is useful for better understanding the active site as well as the practical aspect of pharmaceutical drugs. Below are idealized Line-Weaver Burke plots of different types of inhibitors. Comnetitive Uncomnetitive Mixed +Inh +Inh 4Inh Anh Inh Anh [S] [S] [S] a. How does the value of Vmax for the enzyme compare to the Vmax PP of the inhibited enzyme for: i. Competitive ii. Uncompetitive iii. Mixed b. How does the value of Km for the enzyme compare to the Km PP of the inhibited enzyme for: i. Competitive ii. Uncompetitive iii. Mixed c. For each situation in Model 1, consider an inhibitor that is better than the one shown on the graph. Answer the following questions for each type of inhibition: i. How would the KmPP change? ii. How would the Vmax PP change?Small molecules are used as inhibitors of protein action - as drugs. They most often do this by blocking the active site within the protein. Potential drugs can be screened computationally to determine if they are strongly bound to the protein. Figure 1 shows a possible conformation of a candidate drug molecule, 4-bromo-2- carboxymethylamide-pyrrole (abbreviation: BCMAP) at the active site of a protein (abbreviation: PR). Figure 2 shows the full protein structure whilst figure 3 shows a known inhibitor of the protein at the site, overlayed with another calculated conformer of BCMAP. (c) Outline how you would investigate whether BCMAP would be an effective inhibitor for the protein in competition with the molecules that the protein normally targets, and any solvent. Figure 1. 4-bromo-2-carboxymethylamide-pyrrole (BCMAP) (C, N, O, and Br atoms in yellow, blue, red, and brown, respectively) in the active site of the protein structure.