Sandbox WWC8: Difference between revisions

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== Structural Features ==

The globular NP protein is rich in arginine, serine, and glycine residues. The abundance of arginine residues gives the protein a net positive charge at pH 7. With a predicted pI of 9.3, NP is mainly composed of basic residues, except for a tail domain of the 30 C-terminal residues, which are acidic. The C-tail domain has a pI of 3.7. The NP is a homo 3-mer - A3 with 499 amino acid residues encoded by the Influenza A RNA segment 5.Each homomer provides a binding site for the viral RNA script.

The globular NP protein is rich in arginine, serine, and glycine residues. The abundance of arginine residues gives the protein a net positive charge at pH 7. With a predicted pI of 9.3, NP is mainly composed of basic residues, except for a tail domain of the 30 C-terminal residues, which are acidic. The C-tail domain has a pI of 3.7 [1]. The NP is a homo 3-mer - A3 with 499 amino acid residues encoded by the Influenza A RNA segment 5.Each homomer provides a binding site for the viral RNA script [1].

The homomers fold into a crescent shape with a head and a body domain, where the grove between the two domains hosts the ssRNA binding site on the outer surface of the homomer. For the formation of RNPs, the NP needs to form a coordinated aggregate of three NPs through a process called homo-oligomerization. The C-tail loop, marked in pink in the image below, is critical for this function. Residues 408-419, located at the back of the NP between head and tail domain, form a loop that is the basis of the interface between neighboring NPs. The C-tail loop interlock with the loop binding cavity in the neighboring NP and form a tight binding interaction, featuring both hydrophobic and hydrophilic residues, that keeps the homo 3-mer together. The NP oligomer conformation is especially stabilized by a salt bridge between Arg 416 in the loop and Glu339 in the adjacent NP.

The homomers fold into a crescent shape with a head and a body domain, where the grove between the two domains hosts the ssRNA binding site on the outer surface of the homomer [1,2]. For the formation of RNPs, the NP needs to form a coordinated aggregate of three NPs through a process called homo-oligomerization [2,3]. The C-tail loop, marked in pink in the image below, is critical for this function. Residues 408-419, located at the back of the NP between head and tail domain, form a loop that is the basis of the interface between neighboring NPs. The C-tail loop interlock with the loop binding cavity in the neighboring NP and form a tight binding interaction, featuring both hydrophobic and hydrophilic residues, that keeps the homo 3-mer together. The NP oligomer conformation is especially stabilized by a salt bridge between Arg 416 in the loop and Glu339 in the adjacent NP [2].

[[Image:Structural Features of NP.jpg]]

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====RNA binding activity====

NP binds ssRNA in the RNA binding grove with an affinity of Kd ~20 nM. The binding of ssRNA is not sequence specific and the approximate stoichemetry is 1 NP monomer: 24 ssRNA nucleotides. Although the portions of ssRNA not directly bound in the grove wraps around NP, the RNA is not protected from digestion by RNase.

NP binds ssRNA in the RNA binding grove with an affinity of Kd ~20 nM. The binding of ssRNA is not sequence specific and the approximate stoichemetry is 1 NP monomer: 24 ssRNA nucleotides. Although the portions of ssRNA not directly bound in the grove wraps around NP, the RNA is not protected from digestion by RNase [1].

The RNA binding region (RNA binding grove) has been mapped (via deletion mutagenesis) to cluster around residues located in the N-terminal third of the nucleoprotein. This large region is aided in RNA binding by surrounding regions that affect the binding affinity. Thus, the RNA-binding mechanism of NP is characterized by co-operativity and allosteric regulation.

The RNA binding region (RNA binding grove) has been mapped (via deletion mutagenesis) to cluster around residues located in the N-terminal third of the nucleoprotein. This large region is aided in RNA binding by surrounding regions that affect the binding affinity. Thus, the RNA-binding mechanism of NP is characterized by co-operativity and allosteric regulation [1].

====Nuceloprotein Interactions with Polymerase====

The influenza virus polymerase complex is essential for directing virus replication inside the host cell's nucleus. The viral polymerase complex consists of three sub units, PA,PB1, and PB2 [7]. The polymerase complex directs both, viral RNA replication and viral genome transcription. Additionally, the complex can steal 5' RNA primers from host mRNAs during transcription of viral RNA [10]. NP has been found to have substantial regulatory interaction with PB1 and PB2. The NP interaction with PB2 is host specific and depends on the amino acid sequence found in the C-terminal tail loop region. Thus, the direct interaction between NP and PB2 may be the switch between viral RNA replication and transcription [6].

====Other Binding Interactions====

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[9] B. Tarus, H. Bertrand, G. Zedda, C. Di Primo, S. Quideau, A. Slama-Schwok, Structure-based design of novel naproxen derivatives targeting monomeric nucleoprotein of Influenza A virus, Journal of Biomolecular Structure and Dynamics. 33 (2015) 1899–1912. doi:10.1080/07391102.2014.979230.

10] S. Boivin, S. Cusack, R.W.H. Ruigrok, D.J. Hart, Influenza A Virus Polymerase: Structural Insights into Replication and Host Adaptation Mechanisms, J. Biol. Chem. 285 (2010) 28411–28417. doi:10.1074/jbc.R110.117531.

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@@ Line 9: / Line 9: @@
 == Structural Features ==
-The globular NP protein is rich in arginine, serine, and glycine residues. The abundance of arginine residues gives the protein a net positive charge at pH 7. With a predicted pI of 9.3, NP is mainly composed of basic residues, except for a tail domain of the 30 C-terminal residues, which are acidic. The C-tail domain has a pI of 3.7. The NP is a homo 3-mer - A3 with 499 amino acid residues encoded by the Influenza A RNA segment 5.Each homomer provides a binding site for the viral RNA script.
+The globular NP protein is rich in arginine, serine, and glycine residues. The abundance of arginine residues gives the protein a net positive charge at pH 7. With a predicted pI of 9.3, NP is mainly composed of basic residues, except for a tail domain of the 30 C-terminal residues, which are acidic. The C-tail domain has a pI of 3.7 [1]. The NP is a homo 3-mer - A3 with 499 amino acid residues encoded by the Influenza A RNA segment 5.Each homomer provides a binding site for the viral RNA script [1].
-The homomers fold into a crescent shape with a head and a body domain, where the grove between the two domains hosts the ssRNA binding site on the outer surface of the homomer. For the formation of RNPs, the NP needs to form a coordinated aggregate of three NPs through a process called homo-oligomerization. The C-tail loop, marked in pink in the image below, is critical for this function. Residues 408-419, located at the back of the NP between head and tail domain, form a loop that is the basis of the interface between neighboring NPs. The C-tail loop interlock with the loop binding cavity in the neighboring NP and form a tight binding interaction, featuring both hydrophobic and hydrophilic residues, that keeps the homo 3-mer together. The NP oligomer conformation is especially stabilized by a salt bridge between Arg 416 in the loop and Glu339 in the adjacent NP.
+The homomers fold into a crescent shape with a head and a body domain, where the grove between the two domains hosts the ssRNA binding site on the outer surface of the homomer [1,2]. For the formation of RNPs, the NP needs to form a coordinated aggregate of three NPs through a process called homo-oligomerization [2,3]. The C-tail loop, marked in pink in the image below, is critical for this function. Residues 408-419, located at the back of the NP between head and tail domain, form a loop that is the basis of the interface between neighboring NPs. The C-tail loop interlock with the loop binding cavity in the neighboring NP and form a tight binding interaction, featuring both hydrophobic and hydrophilic residues, that keeps the homo 3-mer together. The NP oligomer conformation is especially stabilized by a salt bridge between Arg 416 in the loop and Glu339 in the adjacent NP [2].
 [[Image:Structural Features of NP.jpg]]
@@ Line 17: / Line 17: @@
 ====RNA binding activity====
-NP binds ssRNA in the RNA binding grove with an affinity of Kd ~20 nM. The binding of ssRNA is not sequence specific and the approximate stoichemetry is 1 NP monomer: 24 ssRNA nucleotides. Although the portions of ssRNA not directly bound in the grove wraps around NP, the RNA is not protected from digestion by RNase.
+NP binds ssRNA in the RNA binding grove with an affinity of Kd ~20 nM. The binding of ssRNA is not sequence specific and the approximate stoichemetry is 1 NP monomer: 24 ssRNA nucleotides. Although the portions of ssRNA not directly bound in the grove wraps around NP, the RNA is not protected from digestion by RNase [1].
-The RNA binding region (RNA binding grove) has been mapped (via deletion mutagenesis) to cluster around residues located in the N-terminal third of the nucleoprotein. This large region is aided in RNA binding by surrounding regions that affect the binding affinity. Thus, the RNA-binding mechanism of NP is characterized by co-operativity and allosteric regulation.
+The RNA binding region (RNA binding grove) has been mapped (via deletion mutagenesis) to cluster around residues located in the N-terminal third of the nucleoprotein. This large region is aided in RNA binding by surrounding regions that affect the binding affinity. Thus, the RNA-binding mechanism of NP is characterized by co-operativity and allosteric regulation [1].
 ====Nuceloprotein Interactions with Polymerase====
+The influenza virus polymerase complex is essential for directing virus replication inside the host cell's nucleus. The viral polymerase complex consists of three sub units, PA,PB1, and PB2 [7]. The polymerase complex directs both, viral RNA replication and viral genome transcription. Additionally, the complex can steal 5' RNA primers from host mRNAs during transcription of viral RNA [10]. NP has been found to have substantial regulatory interaction with PB1 and PB2. The NP interaction with PB2 is host specific and depends on the amino acid sequence found in the C-terminal tail loop region. Thus, the direct interaction between NP and PB2 may be the switch between viral RNA replication and transcription [6].
 ====Other Binding Interactions====
@@ Line 60: / Line 60: @@
 [9] B. Tarus, H. Bertrand, G. Zedda, C. Di Primo, S. Quideau, A. Slama-Schwok, Structure-based design of novel naproxen derivatives targeting monomeric nucleoprotein of Influenza A virus, Journal of Biomolecular Structure and Dynamics. 33 (2015) 1899–1912. doi:10.1080/07391102.2014.979230.
+] S. Boivin, S. Cusack, R.W.H. Ruigrok, D.J. Hart, Influenza A Virus Polymerase: Structural Insights into Replication and Host Adaptation Mechanisms, J. Biol. Chem. 285 (2010) 28411–28417. doi:10.1074/jbc.R110.117531.