Suppose that you have decided to test whether the tyrosine residue of the spikeprotein is important for the binding interaction between these 2 differentproteins. To do so, you decide to mutate the tyrosine to another amino acid andthen test the binding strength of the mutant spike protein to the ACE2 receptor.Which of the following is the best choice for your mutant substitution of thetyrosine residue?mutate to alanine -- small, hydrophobic residuemutate to phenylalanine -- aromatic residue without hydroxyl groupmutate to lysine -- basic amino acidIt's impossible to choose. A snapshot of a portion of the SARS-CoV-2 spike protein bound to the human ACE2 receptor (takenfrom PDB) is shown below. The spike protein is in orange and the ACE2 receptor is in green. Withinthe red-circled region are 2 amino acids connected by a dashed line (added by Dr. David). Theseamino acids are a tyrosine residue from the spike protein and an aspartate residue from the ACE2receptor.wcozed

Amino acids are the building blocks of protein. They are classified into different groups like…

Answered: Suppose that you have decided to test…

Biochemistry

9th Edition

ISBN:9781319114671

Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Chapter1: Biochemistry: An Evolving Science

Section: Chapter Questions

Problem 1P

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There was a study done (Isabel, et al.) on structural analysis of SARS-CoV-2 spike protein. The researchers hypothesized that a mutation in Asp 614 to Gly 614 will result in a loss of four inter-chain destabilizing (i.e., hydrophobic-hydrophilic) contacts. I attached an image that illustrates this (C). My question is: how does this classify as a repelling effect when Asp 614 should be hydrogen bonding with Thr 859? If Asp 614 is mutated to Gly 614, then wouldn't this hydrogen bonding no longer occur? Just not too sure what this hydrophobic-hydrophilic repelling effect is referring to exactly.
The codon change (Gly-12 to Val-12) in human rasH that convertsit to oncogenic rasH has been associated with many types ofcancers. For this reason, researchers would like to develop drugs toinhibit oncogenic rasH. Based on your understanding of the Rasprotein, what types of drugs might you develop? In other words,what would be the structure of the drugs, and how would theyinhibit Ras protein? How would you test the efficacy of the drugs?What might be some side effects?
The ACE2 receptor protein in humans has been getting a lot of press these days, as it apparently serves as a "receptor" for the SARS-CoV-2 coronavirus in addition to its normal functions. This protein has an isoelectric pH of 5.36. Suppose you want to purify this protein to study its properties, with the goal of developing a drug that would block it from binding the virus. Once you have purified the cell surface proteins from your cultured human lung cells away from all the other types of molecules in the cell, and all the cytoplasmic proteins, you might decide to use ion exchange chromatography to separate the ACE2 proteins from other proteins in your sample. If you plan to load your protein mixture onto your ion exchange column in a buffer at pH 7.4 (approximately physiological pH) and you want the ACE2 proteins to bind to the column, should you use a resin with a positive charge or a negative charge? Briefly explain why you chose the resin you selected.
The protein fragments ABS1 and ABS2 of tropomodulin were produced as fusion proteins with chitin binding domain and purified by a chitin column. Explain the principles of this type of affinity chromatography and support it with a self‐drawn figure. This is with regards to Tropomodulin/ F-Actin complex.
Explain the signifi cance of the observation that peptides such as fMet-Leu-Phe “activate” the phagocytotic (particle-engulfi ng) functions of mammalian leukocytes (white blood cells).
The ABO blood group antigens are the terminal sugars covalently linked to the end of the glycolipid in the red blood cellmembrane. The H antigen is the precursor of the A and Bantigens. Individuals with type A blood produce a gene thatcodes for an enzyme that adds N-acetylgalactosamine in ana(1,3) linkage to the Gal* residue in the H antigen. Type Bblood requires that an enzyme add a d-a galactose in an a(1,3) linkage to the Gal*. Draw the structures of the A andB antigens.
Members of the integrin family are the major cell surface receptors for many ECM proteins such as fibronectin. In experimental studies, single integrin heterodimers have been found to assume more than one structural conformation. Describe the relationship between integrin structures and their activities.
Polypeptides with the ER Signal Sequence (MMSFVSLLLVGILFTATEAEQLTKCEVFQ <- one-letter amino acid abbreviations) are targeted to the ER The ER Retrieval tag (KDEL) causes proteins to remain in the ER Protein Q has both an ER signal sequence and the ER retrieval tag.
When human hemoglobin undergoes a mutation, the mutant protein usually does not replace all of the normal HbA in the red blood cells or erythrocytes of the individual. The erythro- cytes contain mixtures of varying amounts of both HbA and the mutant protein depending on the mutation and the individual. Hb Yakima is a mutant human Hb with an Asp-(B99)His mutation. The diagram on the right shows that Hb Yakima was separated by DEAE-cellulose chromatography from HbA with a 0 – 0.1 M linear gradient of NaCl buffered to pH 8.3. Why is chromatog- raphy carried out at pH 8.3? If the isoelectric point of HbA is 6.85, what is the change in total charge caused by the mutation?How does the change in charge explain the chromatography elution profile of the Hb Yakima/HbA mixture? 1,5 -Hb-A Hb -Yakima 1.0 0.5- 20 40 60 80 00 Fraction number O.D578 nm
Which of the following mutations would produce a form of the Ras protein that would be more difficult to inactivate than normal Ras? Briefly explain your reasoning.(i) A mutation that allows Ras to cleave (hydrolyze) GTP more rapidly than usual(ii) A mutation that causes Ras to bind Ras-GAP more tightly than usual(iii) A mutation that causes Ras to cleave (hydrolyze) GTP more slowly than usual
The distal Histidine (His 64) in myoglobin is subjected to three different mutations, this is one of them: H64N. (Histidine to Aparagine) For the mutation, draw a theoretical binding curve and CO relative to the O2 and CO binding curves for wild-type Mb (see example below). Provide a clear rationale for the binding curve.
Consider the now dominant variant of the SARS-CoV-2 called the D614G mutation: a) The mutation changes an Aspartate (D, Asp) to a Glycine (G, Gly) at nucleotide position 614 (that’s why it’s called the D614G mutant) in the S1 subunit of the Spike protein. Using only the information above and a codon table, what are the mRNA codon sequences of the 2019-dominant and 2020-dominant Spike proteins? Note the figure above is not needed toanswer the question. Report in 5’ to 3' orientation __________________________________________ b) What type of substitution is this? In your answer, address the following: • The expected substitution in base sequence (e.g., A à C)• If the mutation is synonymous, nonsynonymous, or a frameshift• If the mutation is a transition or a transversion c) The mutation increases infectivity by reducing the stability of the Spike protein such that it can remain in the open conformation more often. The open conformation increases the chances of binding to the host ACE2…

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