Review



aac6 sequences  (Addgene inc)


Bioz Verified Symbol Addgene inc is a verified supplier  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
    • 92
      Buy from Supplier

    Structured Review

    Addgene inc aac6 sequences
    Figure 1. Approach: from Experimental Evolution to Residue Interactions and 3D Structures The experiments involve repeated rounds of mutation and selection, starting from a single sequence (b-lactamase PSE1, 266 residues; or aminoglycoside acetyltransferase <t>AAC6,</t> 148 residues). In each round, mutations are generated by error-prone PCR, followed by selection in E. coli for functional variants at relatively low antibiotic concentration (6 mg/mL ampicillin [Amp] for PSE1 and 10 mg/mL kanamycin [Kan] for AAC6). A large number of full-length sequences at various rounds are obtained by deep sequencing after selection; here, at rounds 10 and 20 for PSE1, and rounds 2, 4 and 8 for AAC6. Residue interactions are inferred from co-evolution patterns in the selected sequences using the evolutionary couplings (EVcouplings (Marks et al., 2011)) maximum entropy model, which are then used as distance constraints to compute 3D structures using distance geometry and simulated annealing molecular dynamics (Brunger, 2007).
    Aac6 Sequences, supplied by Addgene inc, used in various techniques. Bioz Stars score: 92/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/aac6 sequences/product/Addgene inc
    Average 92 stars, based on 1 article reviews
    aac6 sequences - by Bioz Stars, 2026-05
    92/100 stars

    Images

    1) Product Images from "Protein Structure from Experimental Evolution."

    Article Title: Protein Structure from Experimental Evolution.

    Journal: Cell systems

    doi: 10.1016/j.cels.2019.11.008

    Figure 1. Approach: from Experimental Evolution to Residue Interactions and 3D Structures The experiments involve repeated rounds of mutation and selection, starting from a single sequence (b-lactamase PSE1, 266 residues; or aminoglycoside acetyltransferase AAC6, 148 residues). In each round, mutations are generated by error-prone PCR, followed by selection in E. coli for functional variants at relatively low antibiotic concentration (6 mg/mL ampicillin [Amp] for PSE1 and 10 mg/mL kanamycin [Kan] for AAC6). A large number of full-length sequences at various rounds are obtained by deep sequencing after selection; here, at rounds 10 and 20 for PSE1, and rounds 2, 4 and 8 for AAC6. Residue interactions are inferred from co-evolution patterns in the selected sequences using the evolutionary couplings (EVcouplings (Marks et al., 2011)) maximum entropy model, which are then used as distance constraints to compute 3D structures using distance geometry and simulated annealing molecular dynamics (Brunger, 2007).
    Figure Legend Snippet: Figure 1. Approach: from Experimental Evolution to Residue Interactions and 3D Structures The experiments involve repeated rounds of mutation and selection, starting from a single sequence (b-lactamase PSE1, 266 residues; or aminoglycoside acetyltransferase AAC6, 148 residues). In each round, mutations are generated by error-prone PCR, followed by selection in E. coli for functional variants at relatively low antibiotic concentration (6 mg/mL ampicillin [Amp] for PSE1 and 10 mg/mL kanamycin [Kan] for AAC6). A large number of full-length sequences at various rounds are obtained by deep sequencing after selection; here, at rounds 10 and 20 for PSE1, and rounds 2, 4 and 8 for AAC6. Residue interactions are inferred from co-evolution patterns in the selected sequences using the evolutionary couplings (EVcouplings (Marks et al., 2011)) maximum entropy model, which are then used as distance constraints to compute 3D structures using distance geometry and simulated annealing molecular dynamics (Brunger, 2007).

    Techniques Used: Residue, Mutagenesis, Selection, Sequencing, Generated, Functional Assay, Concentration Assay

    Figure 4. Agreement between Residue Con- tacts Inferred from Experimental Evolution and Contacts in Crystal Structures (A) Agreement versus number of inferred in- teractions (as fraction of sequence length, L) during experimental evolution of PSE1 (left) and AAC6 (right). PSE1 results evaluated for an equal number (4 3 104) of randomly subsampled unique se- quences from rounds 10 and 20 to illustrate change in agreement with increased rounds of mutation and selection, and all (1.5 3 105) unique sequences at round 20 to illustrate change with increased number of sequences. AAC6 similarly assessed for an equal number (105) of randomly subsampled unique se- quences at rounds 2, 4 and 8, and all (1.3 3 106) unique sequences at round 8. Random is the average result obtained with randomly chosen res- idue pairs. (B) Inferred interactions from PSE1 evolution at round 20 (left) and AAC6 evolution at round 8 (right), overlaid on contact maps of crystal structures. In- ferred interactions either agree with monomer (red) or dimer (blue) contacts in the crystal structure (gray or light blue, respectively), or disagree (black). For PSE1, sequence-distal residue interactions between the N- and C-terminal a-helices and b-strands (lower left corner of contact map and indicated on crystal structure of PSE1) are particu- larly crucial constraints for the correct 3D fold via reduction of chain entropy. Dashed line in (A) and results in (B) are at L/2 inferred interactions; agree- ment of > 50% at L/2 often suffices to compute 3D structures (Hopf et al., 2012; Marks et al., 2012). In (A) and (B), residues in the known crystal structure are defined to be in contact if at least one atom- atom distance is < 5 A˚ ; inferred residue-residue interactions are limited to a primary sequence dis- tance > 5 residues.
    Figure Legend Snippet: Figure 4. Agreement between Residue Con- tacts Inferred from Experimental Evolution and Contacts in Crystal Structures (A) Agreement versus number of inferred in- teractions (as fraction of sequence length, L) during experimental evolution of PSE1 (left) and AAC6 (right). PSE1 results evaluated for an equal number (4 3 104) of randomly subsampled unique se- quences from rounds 10 and 20 to illustrate change in agreement with increased rounds of mutation and selection, and all (1.5 3 105) unique sequences at round 20 to illustrate change with increased number of sequences. AAC6 similarly assessed for an equal number (105) of randomly subsampled unique se- quences at rounds 2, 4 and 8, and all (1.3 3 106) unique sequences at round 8. Random is the average result obtained with randomly chosen res- idue pairs. (B) Inferred interactions from PSE1 evolution at round 20 (left) and AAC6 evolution at round 8 (right), overlaid on contact maps of crystal structures. In- ferred interactions either agree with monomer (red) or dimer (blue) contacts in the crystal structure (gray or light blue, respectively), or disagree (black). For PSE1, sequence-distal residue interactions between the N- and C-terminal a-helices and b-strands (lower left corner of contact map and indicated on crystal structure of PSE1) are particu- larly crucial constraints for the correct 3D fold via reduction of chain entropy. Dashed line in (A) and results in (B) are at L/2 inferred interactions; agree- ment of > 50% at L/2 often suffices to compute 3D structures (Hopf et al., 2012; Marks et al., 2012). In (A) and (B), residues in the known crystal structure are defined to be in contact if at least one atom- atom distance is < 5 A˚ ; inferred residue-residue interactions are limited to a primary sequence dis- tance > 5 residues.

    Techniques Used: Residue, Sequencing, Mutagenesis, Selection

    Figure 6. Variation among Computed 3D Structure Models (A) Template modeling scores (TM-scores [Zhang and Skolnick, 2005]) for all computed models during geometric violation filtering iterations. Computed models are sorted along the x axis by TM-score within each iteration. Overall, structures computed with interactions inferred from experi- mentally evolved sequences have the same gen- eral fold as the crystal structure, with TM-scores of > 0.5 for 72% of PSE1 models (690 total models) and for 63% of AAC6 models (720 total models) in the final iteration for both proteins. (B) Structural variation between computed models. The color and radius of each residue is monotonically related to the RMSD of Ca-Ca dis- tances computed from all-versus-all pairwise su- perposition of models in the largest cluster (MaxCluster [Herbert and Sternberg, 2008]) from the final filtering iteration (STAR Methods).
    Figure Legend Snippet: Figure 6. Variation among Computed 3D Structure Models (A) Template modeling scores (TM-scores [Zhang and Skolnick, 2005]) for all computed models during geometric violation filtering iterations. Computed models are sorted along the x axis by TM-score within each iteration. Overall, structures computed with interactions inferred from experi- mentally evolved sequences have the same gen- eral fold as the crystal structure, with TM-scores of > 0.5 for 72% of PSE1 models (690 total models) and for 63% of AAC6 models (720 total models) in the final iteration for both proteins. (B) Structural variation between computed models. The color and radius of each residue is monotonically related to the RMSD of Ca-Ca dis- tances computed from all-versus-all pairwise su- perposition of models in the largest cluster (MaxCluster [Herbert and Sternberg, 2008]) from the final filtering iteration (STAR Methods).

    Techniques Used: Residue



    Similar Products

    aac6 sequences  (Addgene inc)
    92
    Addgene inc aac6 sequences
    Figure 1. Approach: from Experimental Evolution to Residue Interactions and 3D Structures The experiments involve repeated rounds of mutation and selection, starting from a single sequence (b-lactamase PSE1, 266 residues; or aminoglycoside acetyltransferase <t>AAC6,</t> 148 residues). In each round, mutations are generated by error-prone PCR, followed by selection in E. coli for functional variants at relatively low antibiotic concentration (6 mg/mL ampicillin [Amp] for PSE1 and 10 mg/mL kanamycin [Kan] for AAC6). A large number of full-length sequences at various rounds are obtained by deep sequencing after selection; here, at rounds 10 and 20 for PSE1, and rounds 2, 4 and 8 for AAC6. Residue interactions are inferred from co-evolution patterns in the selected sequences using the evolutionary couplings (EVcouplings (Marks et al., 2011)) maximum entropy model, which are then used as distance constraints to compute 3D structures using distance geometry and simulated annealing molecular dynamics (Brunger, 2007).
    Aac6 Sequences, supplied by Addgene inc, used in various techniques. Bioz Stars score: 92/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/aac6 sequences/product/Addgene inc
    Average 92 stars, based on 1 article reviews
    aac6 sequences - by Bioz Stars, 2026-05
    92/100 stars
    		  Buy from Supplier

    Image Search Results


    Figure 1. Approach: from Experimental Evolution to Residue Interactions and 3D Structures The experiments involve repeated rounds of mutation and selection, starting from a single sequence (b-lactamase PSE1, 266 residues; or aminoglycoside acetyltransferase AAC6, 148 residues). In each round, mutations are generated by error-prone PCR, followed by selection in E. coli for functional variants at relatively low antibiotic concentration (6 mg/mL ampicillin [Amp] for PSE1 and 10 mg/mL kanamycin [Kan] for AAC6). A large number of full-length sequences at various rounds are obtained by deep sequencing after selection; here, at rounds 10 and 20 for PSE1, and rounds 2, 4 and 8 for AAC6. Residue interactions are inferred from co-evolution patterns in the selected sequences using the evolutionary couplings (EVcouplings (Marks et al., 2011)) maximum entropy model, which are then used as distance constraints to compute 3D structures using distance geometry and simulated annealing molecular dynamics (Brunger, 2007).

    Journal: Cell systems

    Article Title: Protein Structure from Experimental Evolution.

    doi: 10.1016/j.cels.2019.11.008

    Figure Lengend Snippet: Figure 1. Approach: from Experimental Evolution to Residue Interactions and 3D Structures The experiments involve repeated rounds of mutation and selection, starting from a single sequence (b-lactamase PSE1, 266 residues; or aminoglycoside acetyltransferase AAC6, 148 residues). In each round, mutations are generated by error-prone PCR, followed by selection in E. coli for functional variants at relatively low antibiotic concentration (6 mg/mL ampicillin [Amp] for PSE1 and 10 mg/mL kanamycin [Kan] for AAC6). A large number of full-length sequences at various rounds are obtained by deep sequencing after selection; here, at rounds 10 and 20 for PSE1, and rounds 2, 4 and 8 for AAC6. Residue interactions are inferred from co-evolution patterns in the selected sequences using the evolutionary couplings (EVcouplings (Marks et al., 2011)) maximum entropy model, which are then used as distance constraints to compute 3D structures using distance geometry and simulated annealing molecular dynamics (Brunger, 2007).

    Article Snippet: Plasmids generated in this study that contain ancestral PSE1 and AAC6 sequences have been deposited at Addgene: 135229 and Addgene: 135230, respectively.

    Techniques: Residue, Mutagenesis, Selection, Sequencing, Generated, Functional Assay, Concentration Assay

    Figure 4. Agreement between Residue Con- tacts Inferred from Experimental Evolution and Contacts in Crystal Structures (A) Agreement versus number of inferred in- teractions (as fraction of sequence length, L) during experimental evolution of PSE1 (left) and AAC6 (right). PSE1 results evaluated for an equal number (4 3 104) of randomly subsampled unique se- quences from rounds 10 and 20 to illustrate change in agreement with increased rounds of mutation and selection, and all (1.5 3 105) unique sequences at round 20 to illustrate change with increased number of sequences. AAC6 similarly assessed for an equal number (105) of randomly subsampled unique se- quences at rounds 2, 4 and 8, and all (1.3 3 106) unique sequences at round 8. Random is the average result obtained with randomly chosen res- idue pairs. (B) Inferred interactions from PSE1 evolution at round 20 (left) and AAC6 evolution at round 8 (right), overlaid on contact maps of crystal structures. In- ferred interactions either agree with monomer (red) or dimer (blue) contacts in the crystal structure (gray or light blue, respectively), or disagree (black). For PSE1, sequence-distal residue interactions between the N- and C-terminal a-helices and b-strands (lower left corner of contact map and indicated on crystal structure of PSE1) are particu- larly crucial constraints for the correct 3D fold via reduction of chain entropy. Dashed line in (A) and results in (B) are at L/2 inferred interactions; agree- ment of > 50% at L/2 often suffices to compute 3D structures (Hopf et al., 2012; Marks et al., 2012). In (A) and (B), residues in the known crystal structure are defined to be in contact if at least one atom- atom distance is < 5 A˚ ; inferred residue-residue interactions are limited to a primary sequence dis- tance > 5 residues.

    Journal: Cell systems

    Article Title: Protein Structure from Experimental Evolution.

    doi: 10.1016/j.cels.2019.11.008

    Figure Lengend Snippet: Figure 4. Agreement between Residue Con- tacts Inferred from Experimental Evolution and Contacts in Crystal Structures (A) Agreement versus number of inferred in- teractions (as fraction of sequence length, L) during experimental evolution of PSE1 (left) and AAC6 (right). PSE1 results evaluated for an equal number (4 3 104) of randomly subsampled unique se- quences from rounds 10 and 20 to illustrate change in agreement with increased rounds of mutation and selection, and all (1.5 3 105) unique sequences at round 20 to illustrate change with increased number of sequences. AAC6 similarly assessed for an equal number (105) of randomly subsampled unique se- quences at rounds 2, 4 and 8, and all (1.3 3 106) unique sequences at round 8. Random is the average result obtained with randomly chosen res- idue pairs. (B) Inferred interactions from PSE1 evolution at round 20 (left) and AAC6 evolution at round 8 (right), overlaid on contact maps of crystal structures. In- ferred interactions either agree with monomer (red) or dimer (blue) contacts in the crystal structure (gray or light blue, respectively), or disagree (black). For PSE1, sequence-distal residue interactions between the N- and C-terminal a-helices and b-strands (lower left corner of contact map and indicated on crystal structure of PSE1) are particu- larly crucial constraints for the correct 3D fold via reduction of chain entropy. Dashed line in (A) and results in (B) are at L/2 inferred interactions; agree- ment of > 50% at L/2 often suffices to compute 3D structures (Hopf et al., 2012; Marks et al., 2012). In (A) and (B), residues in the known crystal structure are defined to be in contact if at least one atom- atom distance is < 5 A˚ ; inferred residue-residue interactions are limited to a primary sequence dis- tance > 5 residues.

    Article Snippet: Plasmids generated in this study that contain ancestral PSE1 and AAC6 sequences have been deposited at Addgene: 135229 and Addgene: 135230, respectively.

    Techniques: Residue, Sequencing, Mutagenesis, Selection

    Figure 6. Variation among Computed 3D Structure Models (A) Template modeling scores (TM-scores [Zhang and Skolnick, 2005]) for all computed models during geometric violation filtering iterations. Computed models are sorted along the x axis by TM-score within each iteration. Overall, structures computed with interactions inferred from experi- mentally evolved sequences have the same gen- eral fold as the crystal structure, with TM-scores of > 0.5 for 72% of PSE1 models (690 total models) and for 63% of AAC6 models (720 total models) in the final iteration for both proteins. (B) Structural variation between computed models. The color and radius of each residue is monotonically related to the RMSD of Ca-Ca dis- tances computed from all-versus-all pairwise su- perposition of models in the largest cluster (MaxCluster [Herbert and Sternberg, 2008]) from the final filtering iteration (STAR Methods).

    Journal: Cell systems

    Article Title: Protein Structure from Experimental Evolution.

    doi: 10.1016/j.cels.2019.11.008

    Figure Lengend Snippet: Figure 6. Variation among Computed 3D Structure Models (A) Template modeling scores (TM-scores [Zhang and Skolnick, 2005]) for all computed models during geometric violation filtering iterations. Computed models are sorted along the x axis by TM-score within each iteration. Overall, structures computed with interactions inferred from experi- mentally evolved sequences have the same gen- eral fold as the crystal structure, with TM-scores of > 0.5 for 72% of PSE1 models (690 total models) and for 63% of AAC6 models (720 total models) in the final iteration for both proteins. (B) Structural variation between computed models. The color and radius of each residue is monotonically related to the RMSD of Ca-Ca dis- tances computed from all-versus-all pairwise su- perposition of models in the largest cluster (MaxCluster [Herbert and Sternberg, 2008]) from the final filtering iteration (STAR Methods).

    Article Snippet: Plasmids generated in this study that contain ancestral PSE1 and AAC6 sequences have been deposited at Addgene: 135229 and Addgene: 135230, respectively.

    Techniques: Residue