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The innate immune system relies heavily on the phagocytic action of neutrophils, mobile white blood cells that engulf and degrade bacteria and viruses as the first line of host defense against invading pathogens. One mechanism for eliminating viruses engulfed in the phagosome involves the degradation of viral proteins by neutrophil serine proteases (NSPs) .NSPs, which form part of the chymotrypsin family of serine proteases, cleave viral proteins using a catalytic triad relay system. Originally discovered in granules released by neutrophils, NSP4 is a novel monomeric serine protease that has been studied to elucidate the catalytic mechanism of NSPs. Prior experimental data suggest that NSP4 alters its tertiary structure upon substrate binding and cleaves viral proteins using the acylation reaction shown in Figure 1.
Figure 1 Degradation of viral proteins by acylation of NSP4Computational methods were used to identify the energetic parameters of reactions between NSP4 and synthetic viral proteins. To ensure that simulated reactions resembled physiological conditions, algorithms were adjusted to account for the enzyme being in an aqueous environment. The rate-determining step in the acylation reaction was determined by calculating the changes in free energy in both the enzyme and substrate (Figure 2) .
Figure 2 Free energy profiles of synthetic viral protein cleavageKnowledge of amino acid frequency distribution at an enzymatic active site may facilitate the design of novel active sites and enzyme-specific inhibitors. Researchers analyzed the composition of amino acids that form the NSP4 active site during protein folding to study the characteristics of residues involved in active site formation (Figure 3) .
Figure 3 Frequency distribution of amino acid residues at the NSP4 active site
Adapted from Stapels DA, Geisbrecht BV, Rooijakkers SH. Neutrophil serine proteases in antibacterial defense. Curr Opin Microbiol. 2015;23:42-8.
-As NSP4 folds, the water molecules surrounding it become:

Question

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The innate immune system relies heavily on the phagocytic action of neutrophils, mobile white blood cells that engulf and degrade bacteria and viruses as the first line of host defense against invading pathogens. One mechanism for eliminating viruses engulfed in the phagosome involves the degradation of viral proteins by neutrophil serine proteases (NSPs) .NSPs, which form part of the chymotrypsin family of serine proteases, cleave viral proteins using a catalytic triad relay system. Originally discovered in granules released by neutrophils, NSP4 is a novel monomeric serine protease that has been studied to elucidate the catalytic mechanism of NSPs. Prior experimental data suggest that NSP4 alters its tertiary structure upon substrate binding and cleaves viral proteins using the acylation reaction shown in Figure 1.

Figure 1 Degradation of viral proteins by acylation of NSP4Computational methods were used to identify the energetic parameters of reactions between NSP4 and synthetic viral proteins. To ensure that simulated reactions resembled physiological conditions, algorithms were adjusted to account for the enzyme being in an aqueous environment. The rate-determining step in the acylation reaction was determined by calculating the changes in free energy in both the enzyme and substrate (Figure 2) .

Figure 2 Free energy profiles of synthetic viral protein cleavageKnowledge of amino acid frequency distribution at an enzymatic active site may facilitate the design of novel active sites and enzyme-specific inhibitors. Researchers analyzed the composition of amino acids that form the NSP4 active site during protein folding to study the characteristics of residues involved in active site formation (Figure 3) .

Figure 3 Frequency distribution of amino acid residues at the NSP4 active site
Adapted from Stapels DA, Geisbrecht BV, Rooijakkers SH. Neutrophil serine proteases in antibacterial defense. Curr Opin Microbiol. 2015;23:42-8.
-As NSP4 folds, the water molecules surrounding it become:

Quizplus · Accepted Answer

11ecba2d_0dda_0827_a3bf_07378f1f074d_MD0008_00 The polarity and charge of amino acid residues on the surface of a protein affect the order of the surrounding water molecules, as measured by entropy, ΔS. Increased order (decreased entropy) is expressed as a negative ΔS value whereas decreased order (increased entropy) corresponds to a positive ΔS value. Each water molecule must participate in hydrogen bonds, but the side chains of hydrophobic amino acids cannot hydrogen bond with water. Therefore, water molecules in the vicinity of hydrophobic residues must hydrogen bond with each other instead, and can only do so by forming a rigid, highly ordered network called a solvation layer around the hydrophobic molecule. Hydrophilic amino acids, on the other hand, readily hydrogen bond with water, so formation of a solvation layer around these residues is unnecessary. The water molecules surrounding hydrophilic residues are more disordered than those surrounding hydrophobic residues. Unfolded proteins expose their hydrophobic residues to the aqueous environment, causing the surrounding water molecules to form solvation layers. By contrast, folded proteins tend to hide hydrophobic residues in their interior, away from the surrounding water. Hydrophilic residues remain on the surface of the protein, where they can interact with water without a solvation layer. Therefore, as a protein folds, the water surrounding it becomes more disordered. This is reflected by a positive ΔS value. (Choices A and B) The protein becomes more ordered upon folding, but the question asks for the order of the water molecules surrounding the protein. The water molecules become more disordered when the protein folds. (Choice D) The water molecules become more disordered upon protein folding, but disorder is reflected as a positive ΔS rather than a negative ΔS. Educational objective: Entropy is a measure of the disorder within a system. Increased order is expressed as a negative entropy change whereas increased disorder corresponds to a positive entropy change. The water molecules surrounding folded proteins have higher entropy than those surrounding unfolded proteins because the hydrophobic molecules on the surface of unfolded proteins force water to form a rigid solvation layer.

Passage The Innate Immune System Relies Heavily on the Phagocytic Action