Solution and Crystal Structures of a Sugar Binding Site Mutant of Cyanovirin-N: No Evidence of Domain Swapping  Elena Matei, William Furey, Angela M. Gronenborn  Structure  Volume 16, Issue 8, Pages 1183-1194 (August 2008) DOI: 10.1016/j.str.2008.05.011 Copyright © 2008 Elsevier Ltd Terms and Conditions

Figure 1 NMR Solution and X-ray Structures of Wild-Type and Mutant CV-N (A) Ribbon representations of the monomeric solution structure of wild-type CV-N (PDB accession code 2EZM) and the crystal structure of the domain-swapped dimer (PDB accession code 3EZM). Residue positions changed by mutagenesis in CVNmutDB are indicated by blue spheres. The different polypeptide chains in the domain-swapped dimer are colored green and pink. N and C termini of the chains are marked by N and C, respectively, and the pseudosymmetric domains are labeled AM and BM in the monomer, and AD, BD, A'D and B'D in the domain-swapped dimer. (B) Amino acid sequences of [P51G]CV-N and CVNmutDB. Residues belonging to domains A and B are colored green and pink, respectively. Disulfide bonds are indicated by brackets and residues involved in protein-carbohydrate interactions are underlined in the [P51G]CV-N sequence. Identical amino acids in the aligned sequence repeats are marked by dots. Residues that were mutated in CVNmutDB are colored blue. (C) Ribbon superposition of the NMR solution structures of CVNmutDB (green) and wild-type CV-N (pink). Structure 2008 16, 1183-1194DOI: (10.1016/j.str.2008.05.011) Copyright © 2008 Elsevier Ltd Terms and Conditions

Figure 2 NMR Solution Structure of CVNmutDB (A) Stereo view of the superposition of the final 20 conformer ensemble (PDB accession code 2rp3). Backbone (N, Cα, C′) atoms are shown in green and all side-chain atoms in pink. The disulfide bridges are colored yellow. (B) Stereo view of the region around the P51G mutation. The structures of CVNmutDB and wild-type CV-N are shown in ball and stick representation and colored green and pink, respectively. Note the different positions of the Q50 and N53 side chains. Structure 2008 16, 1183-1194DOI: (10.1016/j.str.2008.05.011) Copyright © 2008 Elsevier Ltd Terms and Conditions

Figure 3 Crystal Structure of CVNmutDB (A) Stereo view illustrating the relative orientation of the two monomers in the asymmetric unit. Each β strand is numbered. (B) View of the composite omit electron density map contoured at 1.7 σ for the region W49 to F54. This region is the hinge in the domain-swapped structure of wild-type CV-N and exhibits a loop conformation in the present monomeric structure. Structure 2008 16, 1183-1194DOI: (10.1016/j.str.2008.05.011) Copyright © 2008 Elsevier Ltd Terms and Conditions

Figure 4 Comparison Between Different Crystal Structures of CV-N (A) Stereo view of backbone superpositions of the two monomeric units of CVNmutDB (green)(PDB accession code 3CZZ), the M4-P51G mutant (black) (PDB accession code 2Z21), and the domain-swapped X-ray structure of wild-type CV-N (pink) (PDB accession code 15LB). All structures are displayed in the same orientation after best fit superpositions of one monomer unit each and the pseudomonomer AB' unit of the domain-swapped dimer. (B) Side-by-side view of the two protein molecules in the asymmetric unit of CVNmutDB (green) and the domain-swapped wild-type CV-N (pink) (PDB accession code 15LB), illustrating the similarity in relative orientation. (C) Protein-protein interfaces for the two monomers of CVNmutDB and the pseudomonomers of wild-type domain-swapped dimer (PDB accession code 1L5B). Similar interactions are present, either between amino acids belonging to different monomers (CVNmutDB) or different chains (wild-type CV-N). Structure 2008 16, 1183-1194DOI: (10.1016/j.str.2008.05.011) Copyright © 2008 Elsevier Ltd Terms and Conditions

Figure 5 Titration of CVNmutDB With Mannose Sugars (A) Isothermal titration of CVNmutDB with Man-3. The titration data for 25 automated injections are shown in the top panel, and the total heat released as a function of the molar ratio of Man-3 versus CVNmutDB is displayed in the bottom panel (black). For comparison, previous titration data obtained for CVNmutDB with Man-9 are shown by a dotted line (Barrientos et al., 2006). (B) Isothermal titration of CVNmutDB with Man-2. The titration data for 20 automated injections are shown in the top panel, and the total heat released as a function of the molar ratio of Man-2 versus CVNmutDB is displayed in the bottom panel. The continuous line represents the nonlinear least-squares best fit to the experimental data using a one site model. (C) NMR titration of CVNmutDB with Man-2. The top right hand panel shows the 1H-15N HSQC chemical shift titration curve (bound–free state) versus ligand/ protein molar ratio. The chemical shift difference is defined as: Δδ = [(Δδ HN) 2 + (ΔδN x 0.17) 2]1/2. The bottom panel shows the superposition of 1H-15N HSQC spectra without and in the presence of 3.5 and 12 equivalents of Man-2 in black, green, and magenta, respectively. Selected resonances that experience large shifts upon addition of the disaccharide are labeled with residue name and number in an expanded view in the two top left panels. Structure 2008 16, 1183-1194DOI: (10.1016/j.str.2008.05.011) Copyright © 2008 Elsevier Ltd Terms and Conditions

Figures 6 Comparison Between Experimental and Predicted RDCs Calculated for Different Models (A) Correlation between 1DobsNH measured for CVNmutDB and 1DcalcNH predicted using the wild-type CV-N solution NMR. The identity of data points exhibiting the largest deviations are indicated by residue type and number. (B) Correlation between 1DobsNH measured for CVNmutDB and 1DcalcNH predicted using the two monomers in the crystal structure of CVNmutDB. Data for monomer 1 and 2 are shown in green and pink, respectively. (C) Correlation between 1DobsNH measured for CVNmutDB and 1DcalcNH predicted using the CVNmutDB solution NMR structure before RDC refinement. Structure 2008 16, 1183-1194DOI: (10.1016/j.str.2008.05.011) Copyright © 2008 Elsevier Ltd Terms and Conditions