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Identification of human immunodeficiency virus type 1 (HIV-1) gp120-binding sites on scavenger receptor cysteine rich 1 (SRCR1) domain of gp340.

Chu Y, Li J, Wu X, Hua Z, Wu Z - J. Biomed. Sci. (2013)

Bottom Line: Five peptides coincide with three loop regions showed the relative high binding index.An alanine substitution scan revealed that Asp34, Asp35, Asn96 and Glu101 in two peptides with the highest binding index are the critical residues in SRCR1 interaction with gp120.We pinpointed the vital gp120-binding regions in SRCR1 and narrowed down the amino acids which play critical roles in contacting with gp120.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Center for Public Health Research, School of Medicine, Nanjing University, Nanjing 210093, Jiangsu Province, PR China.

ABSTRACT

Background: gp340, a member of scavenger receptor cysteine rich family encoded by Deleted in Malignant Brain Tumors 1 (DMBT1), is an important component in innate immune defense. The first scavenger receptor cysteine rich domain (SRCR1) of gp340 has been shown to inhibit HIV-1 infection through binding to the N-terminal flank of the V3 loop of HIV-1 gp120.

Results: Through homology modeling and docking analysis of SRCR1 to a gp120-CD4-X5 antibody complex, we identified three loop regions containing polar or acidic residues that directly interacted with gp120. To confirm the docking prediction, a series of over-lapping peptides covering the SRCR1 sequence were synthesized and analyzed by gp120-peptide binding assay. Five peptides coincide with three loop regions showed the relative high binding index. An alanine substitution scan revealed that Asp34, Asp35, Asn96 and Glu101 in two peptides with the highest binding index are the critical residues in SRCR1 interaction with gp120.

Conclusion: We pinpointed the vital gp120-binding regions in SRCR1 and narrowed down the amino acids which play critical roles in contacting with gp120.

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Related in: MedlinePlus

Docking of SRCR1 with monomeric gp120-CD4-X5 complex. A) The structure of the docked SRCR1. SRCR1 and the gp120 core (in blue) are shown in solid ribbon style. CD4 and X5 are represented in silk ribbon style with orange (CD4), green (X5 light chain) and grey (X5 heavy chain), respectively; B) Electrostatic surface of SRCR1 (left) and the V3-loop of gp120 (right). The molecular surfaces of both SRCR1 and the V3-loop of gp120 are colored according to the calculated electrostatic surface potential with negative charges in blue, neutral in white, and positive charges in red; C) The closer view of the gp120-binding sites. The residues in SRCR1, which make contact with gp120, are shown as sticks in grey, whereas the residues in gp120 are colored in blue; D) The docking frequency of residues 1–109 in SRCR1. Three high docking frequency loop regions 33–36, 73–76 and 94–97 are indicated.
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Figure 2: Docking of SRCR1 with monomeric gp120-CD4-X5 complex. A) The structure of the docked SRCR1. SRCR1 and the gp120 core (in blue) are shown in solid ribbon style. CD4 and X5 are represented in silk ribbon style with orange (CD4), green (X5 light chain) and grey (X5 heavy chain), respectively; B) Electrostatic surface of SRCR1 (left) and the V3-loop of gp120 (right). The molecular surfaces of both SRCR1 and the V3-loop of gp120 are colored according to the calculated electrostatic surface potential with negative charges in blue, neutral in white, and positive charges in red; C) The closer view of the gp120-binding sites. The residues in SRCR1, which make contact with gp120, are shown as sticks in grey, whereas the residues in gp120 are colored in blue; D) The docking frequency of residues 1–109 in SRCR1. Three high docking frequency loop regions 33–36, 73–76 and 94–97 are indicated.

Mentions: Our early study demonstrated that gp340 binding to gp120 was significantly enhanced by the pre-treatment of gp120 with soluble CD4 and that the 17b antibody binding to the gp120-sCD4 complex did not abrogate gp340 binding and vice versa [11]. We suggested that the gp340-binding region on gp120 was occluded or partially occluded on the native gp120 and sCD4 binding induced the exposure of the region, thus allowing high affinity interaction between gp340 and gp120 [11]. Therefore, we speculated that a gp120 in complex with sCD4 would be a favorable model for our docking analysis, Since the gp120-sCD4-17b structure does not contain a V3 sequence [21], a newly published crystal structure of a V3-containing HIV-1 gp120 core in complex with sCD4 and a HIV-1 neutralizing antibody-X5 [15] was selected. X5 and 17b belong to the same class of HIV-1 neutralizing antibodies termed CD4-induced (CD4i) antibodies, which recognize highly conserved epitopes exposed upon CD4 binding. The binding of the CD4i antibodies to gp120 is typically enhanced by the CD4 binding. To provide restrains on docking possibilities, a number of factors were considered. First, the location of the V3 loop and the surface for SRCR1 binding on the trimeric viral spike in native state, as determined by Liu et al. [22], were used to orient the SRCR1 structure in the docking. Second, gp340 is a macromolecule with 14 SRCR domains in tandem order, thus SRCR1 can only be docked to a region outside of the plane formed by the β-sheet on the V3 loop due to the steric hindrance. Figure 2A showed a typically docked complex of SRCR1 and gp120-sCD4-X5. The SRCR structure interacted with gp120 on the open face, near the V3 loop site [11], and the N- and C-termini of SRCR, which link the SRCR1 subunit to the rest of the gp340, were pointed away from the gp120.


Identification of human immunodeficiency virus type 1 (HIV-1) gp120-binding sites on scavenger receptor cysteine rich 1 (SRCR1) domain of gp340.

Chu Y, Li J, Wu X, Hua Z, Wu Z - J. Biomed. Sci. (2013)

Docking of SRCR1 with monomeric gp120-CD4-X5 complex. A) The structure of the docked SRCR1. SRCR1 and the gp120 core (in blue) are shown in solid ribbon style. CD4 and X5 are represented in silk ribbon style with orange (CD4), green (X5 light chain) and grey (X5 heavy chain), respectively; B) Electrostatic surface of SRCR1 (left) and the V3-loop of gp120 (right). The molecular surfaces of both SRCR1 and the V3-loop of gp120 are colored according to the calculated electrostatic surface potential with negative charges in blue, neutral in white, and positive charges in red; C) The closer view of the gp120-binding sites. The residues in SRCR1, which make contact with gp120, are shown as sticks in grey, whereas the residues in gp120 are colored in blue; D) The docking frequency of residues 1–109 in SRCR1. Three high docking frequency loop regions 33–36, 73–76 and 94–97 are indicated.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Figure 2: Docking of SRCR1 with monomeric gp120-CD4-X5 complex. A) The structure of the docked SRCR1. SRCR1 and the gp120 core (in blue) are shown in solid ribbon style. CD4 and X5 are represented in silk ribbon style with orange (CD4), green (X5 light chain) and grey (X5 heavy chain), respectively; B) Electrostatic surface of SRCR1 (left) and the V3-loop of gp120 (right). The molecular surfaces of both SRCR1 and the V3-loop of gp120 are colored according to the calculated electrostatic surface potential with negative charges in blue, neutral in white, and positive charges in red; C) The closer view of the gp120-binding sites. The residues in SRCR1, which make contact with gp120, are shown as sticks in grey, whereas the residues in gp120 are colored in blue; D) The docking frequency of residues 1–109 in SRCR1. Three high docking frequency loop regions 33–36, 73–76 and 94–97 are indicated.
Mentions: Our early study demonstrated that gp340 binding to gp120 was significantly enhanced by the pre-treatment of gp120 with soluble CD4 and that the 17b antibody binding to the gp120-sCD4 complex did not abrogate gp340 binding and vice versa [11]. We suggested that the gp340-binding region on gp120 was occluded or partially occluded on the native gp120 and sCD4 binding induced the exposure of the region, thus allowing high affinity interaction between gp340 and gp120 [11]. Therefore, we speculated that a gp120 in complex with sCD4 would be a favorable model for our docking analysis, Since the gp120-sCD4-17b structure does not contain a V3 sequence [21], a newly published crystal structure of a V3-containing HIV-1 gp120 core in complex with sCD4 and a HIV-1 neutralizing antibody-X5 [15] was selected. X5 and 17b belong to the same class of HIV-1 neutralizing antibodies termed CD4-induced (CD4i) antibodies, which recognize highly conserved epitopes exposed upon CD4 binding. The binding of the CD4i antibodies to gp120 is typically enhanced by the CD4 binding. To provide restrains on docking possibilities, a number of factors were considered. First, the location of the V3 loop and the surface for SRCR1 binding on the trimeric viral spike in native state, as determined by Liu et al. [22], were used to orient the SRCR1 structure in the docking. Second, gp340 is a macromolecule with 14 SRCR domains in tandem order, thus SRCR1 can only be docked to a region outside of the plane formed by the β-sheet on the V3 loop due to the steric hindrance. Figure 2A showed a typically docked complex of SRCR1 and gp120-sCD4-X5. The SRCR structure interacted with gp120 on the open face, near the V3 loop site [11], and the N- and C-termini of SRCR, which link the SRCR1 subunit to the rest of the gp340, were pointed away from the gp120.

Bottom Line: Five peptides coincide with three loop regions showed the relative high binding index.An alanine substitution scan revealed that Asp34, Asp35, Asn96 and Glu101 in two peptides with the highest binding index are the critical residues in SRCR1 interaction with gp120.We pinpointed the vital gp120-binding regions in SRCR1 and narrowed down the amino acids which play critical roles in contacting with gp120.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Center for Public Health Research, School of Medicine, Nanjing University, Nanjing 210093, Jiangsu Province, PR China.

ABSTRACT

Background: gp340, a member of scavenger receptor cysteine rich family encoded by Deleted in Malignant Brain Tumors 1 (DMBT1), is an important component in innate immune defense. The first scavenger receptor cysteine rich domain (SRCR1) of gp340 has been shown to inhibit HIV-1 infection through binding to the N-terminal flank of the V3 loop of HIV-1 gp120.

Results: Through homology modeling and docking analysis of SRCR1 to a gp120-CD4-X5 antibody complex, we identified three loop regions containing polar or acidic residues that directly interacted with gp120. To confirm the docking prediction, a series of over-lapping peptides covering the SRCR1 sequence were synthesized and analyzed by gp120-peptide binding assay. Five peptides coincide with three loop regions showed the relative high binding index. An alanine substitution scan revealed that Asp34, Asp35, Asn96 and Glu101 in two peptides with the highest binding index are the critical residues in SRCR1 interaction with gp120.

Conclusion: We pinpointed the vital gp120-binding regions in SRCR1 and narrowed down the amino acids which play critical roles in contacting with gp120.

Show MeSH
Related in: MedlinePlus