LAB #2- Protein Structure and Homology (Lauren R

12 mM of protein A is combined with 6 mM of ligand X in water. After the protein-ligand complex binding reaches equilibrium, you measure that the free ligand concentration is 3 mM and the concentration of protein-ligand complex is 3 mM. What is the Kd for protein A? Although they would be in mM, do not include units in your answer, only the number as a whole integer.

Which of the following statements are true?   Electrostatic interactions are the dominant forces in protein molecular recognition. When two proteins form a complex there is an unfavorable loss of rotational-translational entropy. Protein-protein interfaces are most often dry. The exclusion of water results in an unfavorable loss in rotational-translational entropy. The free energy change associated with the formation of an enzyme-substrate complex almost always results in an unfavorable reduction in conformational entropy of the proteins. Burial of an uncompensated positive charge inside proteins is usually unfavorable. So-called van der Waals’ interactions are essentially electrostatic in origin. Steric complementarity of the two partners forming a complex is essential to achieve optimal free energy of binding. Structural models of proteins obtained from low temperature crystallography are excellent descriptions of all biochemically relevant aspects of their function.

Currently, aspartic acid is forming an ionic interaction with arginine in a protein. Part a) If arginine is replaced with glutamic acid, would the ionic interaction have its stability increased, decreased, or have no effect on the ionic interaction? Part b) If arginine is replaced with Lysine, would the ionic interaction have its stability increased, decreased, or have no effect on the ionic interaction? Part c) If arginine is replaced with isoleucine, would the ionic interaction have its stability increased, decreased, or have no effect on the ionic interaction?

Denaturation of Proteins The following are four levels of protein structures. Identify the inter- and intramolecular forces of attractions that stabilized each level. Level of Protein Structure Forces of Attraction Present Primary   Secondary   Tertiary   Quaternary   2.) What is denaturation? 3.) What are denaturing agents? Give three examples and describe their effects on protein. 4.) Differentiate reversible and irreversible denaturation. 5.)Why is 70% ethanol is more effective than 100% ethanol to kill bacteria?

For the binding of a ligand to a protein, what is the relationship between the Ka (association constant), the Kd (dissociation constant), and the affinity of the protein for the ligand?

Consider protein folding that results when the following components interact:   Where the solution is at a pH of 7, green (thick-dotted line) represents aspartic acid (R group contains a carboxylic acid with pKa = 4), orange (thick-solid line) represents lysine (R group contains an amine with pKa = 10), and blue (thin-solid line) represents hydrophilic groups. Rank the three complexes in order from lowest to highest dissociation constants Kd (low Kd values correspond to good binding constants and low energy, while high Kd values correspond to low binding constants and high energy) as determined by intermolecular charge-charge interactions. For those complexes with charge-charge interactions being equal, look at the possibility for the formation of hydrogen bonds via carboxylic acid dimers (only possible when the carboxylic acid is protonated) which are low energy structures.

In the protein denaturation experiment, which of the following can be a consequence of the air bubbles in the viscometry run for an aqueous solution of protein with a denaturant?a. Increased t0b. Decreased t0c. Increased nspd. Decreased nspAll of the statements about protein denaturation are true EXCEPT:a. The viscosity of linear proteins is greater than that of the globular proteins.b. Only the BME can disrupt a covalent bond while the other denaturants can just disrupt non-covalent bonds.c. Protein renaturation is possible but in some cases protein denaturation proceeds to protein degradation. d. Protein denaturation generally disrupts tertiary or quaternary structures only

Can Hydrophobic Interaction Bead Chromatography be used to isolate Protein X from muscle tissue if Protein X contains many hydrophobic regions? Explain the process of how to isolate Protein X from muscle tissue.

Two proteins, A and B, bind to the same ligand, L, with the binding curvesshown below. What is the dissociation constant, Kd , for each protein? Which protein (A or B) has a greater affinity for ligand L?

1. In a protein, why does when Ala is replaced with Ile, it loses its activity but when Lys is replaced by Arg and Leu to Ile, it only has little effect on protein structure and function? Explain. 2. Why do proteins cannot be denatured reversibly when they are chemically altered to change the chemical composition of certain side chains? Explain.

What are hydrophobic interactions? What are two ways that hydrophobic interactions might impact protein structure and subcellular localization.

Consider the following properties of the protein components of a sample mixture as provided in the table below: 1. if the mixture is subjected to gel filtration chromotography which protein component elute first? 2. if the mixture is subjected to isoelectric focusing which protein will stop m oving nearest to the positive electrode? 3. if the mixture is subjected to cation-exchange chromotography using a buffer at ph 7 which protein will bind to the resin? 4.if the mixture is subjected to SDS-PAGE which protein will be at bottomost portion of gel? 5.if the mixture is subjected to hydrophobic interaction chromotography which protein will bind most strongly to the resin?

Many plasma proteins found in an aqueous environment are globular in shape. Which amino acid side chains would you expect to find on the surface of a globular protein and in contact with the aqueous environment? Which would you expect to find inside, shielded from the aqueous environment? Explain. Q.) Arg

Two proteins bind to the same ligand with the following Kd's. Protein 1: 10 μΜProtein 2: 100 nM Which protein would be bound to more ligand at a ligand concentration of 10 μM? (Assume a limiting concentration of each protein)

Using the picture provided, can you please help me with... A) which Amino Acids are Hydrogen Bond Donors? B) the 5 compouns that are most stable in the cell membrane? C) the 4 compounds that are most soluble in water? Perhaps the names of these different Amino Acids? Thank You!!

A hypothetical protein has a molar mass of 23,300 Da. Assume that the average molar mass of an amino acid is 120. • How many amino acids are present in this hypothetical protein? • What is the minimum number of codons present in the mRNA that codes for this protein? • What is the minimum number of nucleotides needed to code for this protein?

Which of the following must be true based on the data below for ligand L binding to protein A and to protein B? Choice 1 of 4:Protein A binds at least 2 molecules of ligand L. Choice 2 of 4:The Kd for ligand binding to B is approximately 4 micromolar. Choice 3 of 4:When exposed to ligand L, protein A reaches maximal binding faster than does protein B. Choice 4 of 4:Protein B must adopt at least 2 different conformations with different binding affinities.

Which of the following statements best describe(s) the mechanism by which correct protein folding takes place once the misfolded protein binds the open ring of groEL? Select all that apply.     The groEL ring closes to isolate the protein and provide enough time for the protein to properly fold on its own.     b and d     The groEL ring closes to provide a hydrophilic space to isolate the protein and inhibit its aggregation with others until properly folded.     The groEL ring closes to isolate the protein and provide steric hindrance that mechanically refolds the protein.     The groEL ring closes to isolate the protein and decode the information necessary to achieve the correct three-dimensional structure.     None of the above   I picked "The groEL ring closes to provide a hydrophilic space..." but it was incorrect..

Loop regions play important roles in the secondary structure of protein. Define loop  region and give three (3) of the roles

An intermediate folding stage seen in protein denaturation or renaturation is called : a) domain  b)  motif   c)  subunit  d)  molten globule Proteins which do not renature spontaneously when denaturation conditions are removed may need the assistance of: a) a prosthetic group b)  a higher salt concentration   c)  a lower temperature  d)  a chaperone protein The information needed for correct protein folding is encoded in: a) the surrounding molecules  b)  the protein’s amino acid sequence  c)  the pH of the aqueous medium  d)  the electrolyte composition of the aqueous solution

Many plasma proteins found in an aqueous environment are globular in shape. Which amino acid side chains would you expect to find on the surface of a globular protein and in contact with the aqueous environment? Which would you expect to find inside, shielded from the aqueous environment? Explain. Q.) Ser

provide examples of the levels of protein structure for mevalonate kinase (2HFU) provide the levels of protein structure (primary, secondary, tertiary, etc.) for mevalonate kinase (2HFU)

Peptides     and     small     proteins     fold     spontaneously     in     aqueous     solution     at     room    temperature.     Thus,     for     a     small     protein     in     water,     we     can     say ΔG FOLD < 0.          Denoting     the    unfolded    protein    as    Unf and    the    folded    protein    as    Fld,    we    can    write    the    following    equation:Unf(aq)--DELTA G FOLD----> Fld(aq)Considering    the    transition    from    the    unfolded    state    (in    which    there    are    many    possible    conformations)    to    the    folded    state    (only    one    conformation),    there    is    clearly    a    decrease in    the    entropy    of    the    protein.    However,    protein    folding    is    (correctly)    described    as    an    entropically    driven    process.a) Resolve    this    apparent    paradox    by    identifying    the    enthalpy (ΔH)    and    entropy (−TΔS)components    involved    in    protein…

Three different ligands, Ligand Q, Ligand T, and Ligand W, bind to the same protein but with different affinity: The association constant (Ka) for the binding of Ligand Q to the protein is 0.033 nM-1. The fractional saturation (Y) of the protein is 0.20 when the concentration of Ligand T is 1.25 nM. The fractional saturation (Y) of the protein is 0.80 when the concentration of Ligand W is 72 nM. Given this information,  Calculate Kd for the binding of each ligand to this protein. Which ligand binds with greatest affinity? Which ligand binds with the lowest affinity?

detail how cation exchange chromatography works and what you would use to elute your target protein. What protein information would you need to facilitate this approach? Would you need to do any protein engineering to utilize cation exchange chromatography, justify your answer?

Effect of intramolecular and intermolecular forces of attraction to protein folding?

The given protein, Protein X, is a heterotrimer - meaning it is a multimeric protein consisting of different polypeptide chains. Its molecular weight is 200 kDa.  Using SDS-PAGE, the protein was characterized and the following profile is the result (attached in the picture).   1: Standard Protein Ladder 2: Protein X solution 3: Protein X solution + β-mercaptoethanol   Determine the molecular weights of the three subunits of protein X based on the gel profile. Write the MW of each subunit and explain the obtained answer.

What is binding energy? What do negative and less negative energies represent? How does this relate to protein function?

What is Protein folding? Give at least 3 diseases that results from protein misfolding. Explain each.   Can you give me a brief explanation about this question? Not less than 3 sentences.

Consider two proteins, Protein A and Protein B: A is a monomeric protein, whereas B is a subunit of a homo-tetrameric protein. Both A and B are soluble. Additionally, both A and B have similar 3D structures. What differences would you expect to see between the amino acids exposed on the surfaces of A and B? Explain the reasons for the differences observed.

pls answer the following question. -Which amino acids contain the following?a.sulfur/sulfhydryl group b. aromatic group c. imidazole ring d. guanidine group e. indole group -Classify the following proteins according to their biological function: casein, albumin gluten, and myoglobin. -Which levels of protein structure organization are lost during hydrolysis and denaturation? -What is the Beer-Lambert's Law? Why is it relevant to the quantitative analysis of proteins? -What are the other protein components of milk aside from casein?