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alphafold-predicted structures  (Molecular Dynamics Inc)

 
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    Molecular Dynamics Inc alphafold-predicted structures
    Alphafold Predicted Structures, supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 90 stars, based on 1 article reviews
    alphafold-predicted structures - by Bioz Stars, 2026-10
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    Article Title: pH-Dependent Membrane Binding Specificity of Synaptogyrins 1-3 with Distinct Isoelectric Points (pI) Identified by Structural Bioinformatics and Molecular Dynamics
    Article Snippet: Molecular dynamics simulations were performed on the AlphaFold-predicted structures to ensure a consistent comparison.



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    protein structures predicted by alphafold  (Deepmind Technologies Ltd)
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    Image Search Results


    CbbM_base: S162P, G422R, C6: H127V, M140A, K247A, H251A, Q392E, S432T + S162P, G422R, Ad1: H127V, K247A, H251A, Q392E, S432T, W114I + S162P, G422R. ( A ) Selectivity values of selected CbbM variants. (B ) Carboxylation rate constant ( k cat C ). ( C ) Oxygenation rate constant ( k cat O ). ( D ) Binding constant of CO2 in absence of oxygen, ( E ) of CO2 in air, ( F ) binding constant of O2. ( G ) Catalytic efficiency of carboxylation reaction in absence of air, ( H ) of carboxylation reaction in air, ( I ) catalytic efficiency of oxygenation reaction. All catalytic parameters were determined using a 14 CO2 fixation assay with four replicates. Statistical significance was assessed using a one-way ANOVA followed by Tukey’s multiple comparisons test ( J ) Visualization of important residues and active site in a CbbM model (AlphaFold). The dimers are shown in blue and yellow ( K ) Visualization of CbbM model displaying the location of residues mutated in variant Ad1. ( L ) Residue W114 (green) in CbbM constricts a tunnel (blue) in the dimer interface, connecting the two active sites.

    Journal: bioRxiv

    Article Title: The fitness landscape of a Form II rubisco in a photosynthetic bacterium guides engineering of oxygen tolerance

    doi: 10.64898/2025.12.07.690893

    Figure Lengend Snippet: CbbM_base: S162P, G422R, C6: H127V, M140A, K247A, H251A, Q392E, S432T + S162P, G422R, Ad1: H127V, K247A, H251A, Q392E, S432T, W114I + S162P, G422R. ( A ) Selectivity values of selected CbbM variants. (B ) Carboxylation rate constant ( k cat C ). ( C ) Oxygenation rate constant ( k cat O ). ( D ) Binding constant of CO2 in absence of oxygen, ( E ) of CO2 in air, ( F ) binding constant of O2. ( G ) Catalytic efficiency of carboxylation reaction in absence of air, ( H ) of carboxylation reaction in air, ( I ) catalytic efficiency of oxygenation reaction. All catalytic parameters were determined using a 14 CO2 fixation assay with four replicates. Statistical significance was assessed using a one-way ANOVA followed by Tukey’s multiple comparisons test ( J ) Visualization of important residues and active site in a CbbM model (AlphaFold). The dimers are shown in blue and yellow ( K ) Visualization of CbbM model displaying the location of residues mutated in variant Ad1. ( L ) Residue W114 (green) in CbbM constricts a tunnel (blue) in the dimer interface, connecting the two active sites.

    Article Snippet: The structure of the designed variants used for tunnel analysis were predicted using the AlphaFold Protein Structure Database prediction server (DeepMind/EMBL-EBI) ( ).

    Techniques: Binding Assay, Variant Assay, Residue