Passage 10: N Protein
The N protein is a structurally heterogeneous, 419-amino acid-long, multidomain RNA-binding protein. Like other coronaviruses, the N protein also has
two conserved, independently folded domains, namely the N-terminal domain
(NTD) and the C-terminal domain (CTD). These two domains are connected by an
inherently disordered region (IDR) called the central linking region (LKR). The LKR
includes a Ser/Arg (SR)-rich region, which contains putative phosphorylation sites.
In addition, there are two IDRs on both sides of the NTD and CTD, which are called
N-arm and C-tail. NTD is responsible for RNA binding, CTD is responsible for RNA
binding and dimerization, and IDR is responsible for regulating the RNA-binding
activity and oligomerization of NTD and CTD.
NTD takes the shape of a right-handed fist. It consists of a four-strand antiparallel
β-fold core subdomain. The N protein plays a key role in the viral life cycle by
binding to the viral RNA genome and packing it into a helical ribonucleocapsid
(RNP) complex. This process is crucial for the assembly of the viral particle and its
subsequent release from the host cell. This process is seen in Figure 1.
Many RNA-binding proteins, especially those with a high proportion of inherently
disordered regions, participate in liquid-liquid phase separation (LLPS). The protein
LLPS is a physical and chemical phenomenon that is considered to be the key
mechanism for organizing macromolecules, such as proteins and nucleic acids, into
membrane-free organelles. These membrane cell compartments are dynamically
assembled by LLPs and endow cells with the important ability to initiate biological
functions or responses to a range of pressures. After RNA virus infection, LLPS
mediates the formation of stress granules and P-bodies. These substances play an
important role in antiviral immunity by inhibiting the translation of viral mRNA and
promoting RNA degradation. LLPS is also considered to be the key to virus assembly.
According to the passage, which of the following could be functions of
proteins?
I. Enzymatic reactions
II. Nucleotide processing
III. Cell organization
A) II and III
B) I and III
C) only III
D) I, II, and III
Correct answer: D. Since this is a Roman numeral question, it’s
important to consider the option that is the most prevalent in the answer choices,
which is III, since it appears in every answer. If a statement appears in every answer,
then it is automatically part of your answer, and there is no need to evaluate
it. However, for the purpose of explanation, the following is the rationale as to
why it is correct. Since the passage states that “the protein LLPS is a physical
and chemical phenomenon that is considered to be the key mechanism for
organizing macromolecules, such as proteins and nucleic acids, into membranefree organelles,” the proteins have a nonenzymatic function of just organizing the
organelles in membrane-less organelles. This shows that proteins are involved in
cell organization and, more importantly, structuring the cell with different cellular
components. This makes statement III correct. When analyzing statement II, we
have to consider that the passage states that “the N protein plays a key role in
the viral life cycle by binding to the viral RNA genome and packing it into a helical
ribonucleocapsid (RNP) complex.” Since proteins can fold the viral RNA genome
and help make it more condensed, they play a vital role in viral development and
nucleotide processing. This makes the statement true. When analyzing statement I,
we have to remember that there are many examples of proteins acting as enzymes,
and enzymes are a large class of proteins in general biology, thus making statement
I true. Enzymes are just biological protein catalysts, which makes D the right answer.
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