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Accelrys build mutants protocol of discovery studio 3.5
Build Mutants Protocol Of Discovery Studio 3.5, supplied by Accelrys, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/build+mutants+protocol+of+discovery+studio+3%2E5/built+mutants+protocol+biovia+discovery+studio+2019/pmc08762014__gutjnl___2020___323703supp003-104-12-15
Average 90 stars, based on 1 article reviews

build mutants protocol of discovery studio 3.5 - by Bioz Stars, 2026-10

90/100 stars

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Mutagenesis:

Article Title: Impact of NUDT15 polymorphisms on thiopurines-induced myelotoxicity and thiopurines tolerance dose
Article Snippet: The Val18Ile, Arg139His and Arg139Cys mutant models were constructed using the Build Mutants protocol of Discovery Studio 3.5 (Accelrys Inc., USA).

Article Title: Genomic evolution and diverse models of systemic metastases in colorectal cancer
Article Snippet: The C206Y mutation model was constructed using the Build Mutants protocol of Discovery Studio 3.5 (Accelrys Inc., USA).

Construct:

Image Search Results

(A) The quaternary structure (PDB accession no: 1XWO) and (B) the A-B dimeric pairs from diagonal subunits. Monomers of A, B, C and D are colored as green, blue, yellow and gray, respectively. Residues of K315 and W74/W169 are highlighted as CPK and colored as magenta and yellow, respectively. (C) Superimposition of wild-type and K315A mutant proteins present as green and grey color, respectively. A expand view of the interactions of K315 at the interface of A and B subunit is highlighted in (D). Residues of K315 and A315 are displayed as stick models. The interactions are present by dashed green lines.

Journal: PLoS ONE

Article Title: Lys-315 at the Interfaces of Diagonal Subunits of δ-Crystallin Plays a Critical Role in the Reversibility of Folding and Subunit Assembly

doi: 10.1371/journal.pone.0145957

Figure Lengend Snippet: (A) The quaternary structure (PDB accession no: 1XWO) and (B) the A-B dimeric pairs from diagonal subunits. Monomers of A, B, C and D are colored as green, blue, yellow and gray, respectively. Residues of K315 and W74/W169 are highlighted as CPK and colored as magenta and yellow, respectively. (C) Superimposition of wild-type and K315A mutant proteins present as green and grey color, respectively. A expand view of the interactions of K315 at the interface of A and B subunit is highlighted in (D). Residues of K315 and A315 are displayed as stick models. The interactions are present by dashed green lines.

Article Snippet: The structural model was used as a template to build the K315A mutant model using the build mutant protocol (Accelrys Discovery Studio 3.5, Accelrys Inc.).

Techniques: Mutagenesis

Changes in average emission wavelength (AEW) of tryptophan fluorescence are represented as a function of GdmCl (A) and urea (B) concentration. (C) The integrated area of the fluorescence emission spectrum of ANS at varied urea concentration. The labels of (●) and (○), and (▲) and (∆) represent the unfolding and refolding of wild-type and K315A mutant protein, respectively. In (B) and (C), the dark or grey open circles and triangles represent the refolding transition from 3.5 or 4 M urea denatured wild-type and 2.5 or 6 M urea denatured mutant protein, respectively. The (■) and (□) in (B) represent the changes of mean residue of ellipticity (MRE) in the unfolding of wild-type and mutant protein, respectively. The protein concentrations used in the assays were 0.03, 0.2 and 0.1 mg/mL for tryptophan fluorescence, CD and ANS fluorescence measurements, respectively.

Journal: PLoS ONE

Article Title: Lys-315 at the Interfaces of Diagonal Subunits of δ-Crystallin Plays a Critical Role in the Reversibility of Folding and Subunit Assembly

doi: 10.1371/journal.pone.0145957

Figure Lengend Snippet: Changes in average emission wavelength (AEW) of tryptophan fluorescence are represented as a function of GdmCl (A) and urea (B) concentration. (C) The integrated area of the fluorescence emission spectrum of ANS at varied urea concentration. The labels of (●) and (○), and (▲) and (∆) represent the unfolding and refolding of wild-type and K315A mutant protein, respectively. In (B) and (C), the dark or grey open circles and triangles represent the refolding transition from 3.5 or 4 M urea denatured wild-type and 2.5 or 6 M urea denatured mutant protein, respectively. The (■) and (□) in (B) represent the changes of mean residue of ellipticity (MRE) in the unfolding of wild-type and mutant protein, respectively. The protein concentrations used in the assays were 0.03, 0.2 and 0.1 mg/mL for tryptophan fluorescence, CD and ANS fluorescence measurements, respectively.

Article Snippet: The structural model was used as a template to build the K315A mutant model using the build mutant protocol (Accelrys Discovery Studio 3.5, Accelrys Inc.).

Techniques: Fluorescence, Concentration Assay, Mutagenesis, Residue

The continuous sedimentation coefficient distribution of (A) wild-type and (B) K315A mutant protein at different urea concentration were shown. Peaks in grey color represent the unfolded wild-type and mutant protein in 0, 2.5, 3, 3.5 and 4.5 M urea and in 0, 0.25, 0.7, 1.3, 1.5, 2, 2.5, 3.5 and 4.5 M urea, respectively. Wild-type and mutant protein denatured in 3.5 and 2.5 M urea were diluted to final 0.6 and 0.3 M urea, respectively, in 50 mM Tris-acetic acid buffer, pH 7.5, were shown as dark gray peaks. The protein concentration used in all assays was 0.2 mg/mL.

Journal: PLoS ONE

Article Title: Lys-315 at the Interfaces of Diagonal Subunits of δ-Crystallin Plays a Critical Role in the Reversibility of Folding and Subunit Assembly

doi: 10.1371/journal.pone.0145957

Figure Lengend Snippet: The continuous sedimentation coefficient distribution of (A) wild-type and (B) K315A mutant protein at different urea concentration were shown. Peaks in grey color represent the unfolded wild-type and mutant protein in 0, 2.5, 3, 3.5 and 4.5 M urea and in 0, 0.25, 0.7, 1.3, 1.5, 2, 2.5, 3.5 and 4.5 M urea, respectively. Wild-type and mutant protein denatured in 3.5 and 2.5 M urea were diluted to final 0.6 and 0.3 M urea, respectively, in 50 mM Tris-acetic acid buffer, pH 7.5, were shown as dark gray peaks. The protein concentration used in all assays was 0.2 mg/mL.

Article Snippet: The structural model was used as a template to build the K315A mutant model using the build mutant protocol (Accelrys Discovery Studio 3.5, Accelrys Inc.).

Techniques: Sedimentation, Mutagenesis, Concentration Assay, Protein Concentration

The sedimentation velocity experiments were performed and presented as the c( s , f / f o ) distribution for (A) wild-type, (B) and (C) K315A protein in the absence and presence of 1.5 M urea, respectively. (D), K315A protein dissociated in 1.5 M urea was diluted to final of 0.26 M urea in 50 mM Tris-acetic acid buffer (pH 7.5).

Journal: PLoS ONE

Article Title: Lys-315 at the Interfaces of Diagonal Subunits of δ-Crystallin Plays a Critical Role in the Reversibility of Folding and Subunit Assembly

doi: 10.1371/journal.pone.0145957

Figure Lengend Snippet: The sedimentation velocity experiments were performed and presented as the c( s , f / f o ) distribution for (A) wild-type, (B) and (C) K315A protein in the absence and presence of 1.5 M urea, respectively. (D), K315A protein dissociated in 1.5 M urea was diluted to final of 0.26 M urea in 50 mM Tris-acetic acid buffer (pH 7.5).

Article Snippet: The structural model was used as a template to build the K315A mutant model using the build mutant protocol (Accelrys Discovery Studio 3.5, Accelrys Inc.).

Techniques: Sedimentation

Specific activity of δ-crystallin under the denaturant effect.

Journal: PLoS ONE

Article Title: Lys-315 at the Interfaces of Diagonal Subunits of δ-Crystallin Plays a Critical Role in the Reversibility of Folding and Subunit Assembly

doi: 10.1371/journal.pone.0145957

Figure Lengend Snippet: Specific activity of δ-crystallin under the denaturant effect.

Article Snippet: The structural model was used as a template to build the K315A mutant model using the build mutant protocol (Accelrys Discovery Studio 3.5, Accelrys Inc.).

Techniques: Activity Assay, Mutagenesis

(A) Changes in average emission wavelength (AEW) of tryptophan fluorescence and (B) the integrated area of the fluorescence emission spectrum of ANS are presented as a function of GdmCl concentration. Monomeric K315A mutant δ-crystallin was incubated in 1.5 M urea before introducing varied GdmCl concentration. The labels of (●) and (○) represent the unfolding and refolding of monomeric K315A mutant protein, respectively. The (▲) and (∆) in (B) are the refolding transition from 3 and 0.8 M GdmCl denatured monomeric protein, respectively. The solid line in (A) is the best fitted result. The fitting residuals are shown as open triangles in (A). (C) The non-denaturing gel electrophoresis. Lanes 1 and 2 represent the wild-type and mutant protein without denaturant treatment, respectively. Samples from refolding of 5 M GdmCl denatured wild-type and mutant protein for time period of zero or overnight are shown in lanes 3–4 and 5–6, respectively. The protein concentrations used in the assays were 0.03, 0.1 and 0.1 mg/mL for (A), (B) and (C), respectively.

Journal: PLoS ONE

Article Title: Lys-315 at the Interfaces of Diagonal Subunits of δ-Crystallin Plays a Critical Role in the Reversibility of Folding and Subunit Assembly

doi: 10.1371/journal.pone.0145957

Figure Lengend Snippet: (A) Changes in average emission wavelength (AEW) of tryptophan fluorescence and (B) the integrated area of the fluorescence emission spectrum of ANS are presented as a function of GdmCl concentration. Monomeric K315A mutant δ-crystallin was incubated in 1.5 M urea before introducing varied GdmCl concentration. The labels of (●) and (○) represent the unfolding and refolding of monomeric K315A mutant protein, respectively. The (▲) and (∆) in (B) are the refolding transition from 3 and 0.8 M GdmCl denatured monomeric protein, respectively. The solid line in (A) is the best fitted result. The fitting residuals are shown as open triangles in (A). (C) The non-denaturing gel electrophoresis. Lanes 1 and 2 represent the wild-type and mutant protein without denaturant treatment, respectively. Samples from refolding of 5 M GdmCl denatured wild-type and mutant protein for time period of zero or overnight are shown in lanes 3–4 and 5–6, respectively. The protein concentrations used in the assays were 0.03, 0.1 and 0.1 mg/mL for (A), (B) and (C), respectively.

Article Snippet: The structural model was used as a template to build the K315A mutant model using the build mutant protocol (Accelrys Discovery Studio 3.5, Accelrys Inc.).

Techniques: Fluorescence, Concentration Assay, Mutagenesis, Incubation, Nucleic Acid Electrophoresis

Thermodynamic parameters for K315A mutant δ-crystallin.

Journal: PLoS ONE

Article Title: Lys-315 at the Interfaces of Diagonal Subunits of δ-Crystallin Plays a Critical Role in the Reversibility of Folding and Subunit Assembly

doi: 10.1371/journal.pone.0145957

Figure Lengend Snippet: Thermodynamic parameters for K315A mutant δ-crystallin.

Article Snippet: The structural model was used as a template to build the K315A mutant model using the build mutant protocol (Accelrys Discovery Studio 3.5, Accelrys Inc.).

Techniques: Mutagenesis

(A) Light scattering measurement. Monomeric K315A mutant δ-crystallin was incubated in 1.5 M urea before introducing varied GdmCl concentration. Refolding of 0.84, 3 and 5 M GdmCl denatured monomeric K315A mutant protein by dilution with 50 mM Tris-acetic acid buffer (pH7.5) or the buffer containing 1.5 M urea are shown as (●, ▲ and ■) or (○, ∆, and □), respectively. The label of (♦) represents refolding of 0.84 M GdmCl denatured monomers by dilution with buffer including αA-crystallin. αA-Crystallin alone in 1.5 M urea and 0.84 M GdmCl is shown as (◊). The protein concentrations of monomeric K315A and αA-crystallin used in the assays were 0.1 and 0.5 mg/mL, respectively. (B) The fluorescence spectrum of ThT were shown from refolding of 0.84 (dark), 3 (gray) and 5 M (dark gray) GdmCl denatured monomeric K315A mutant protein by dilution with buffer and incubated for zero (solid-line), 1 (dash-line) or 2 (dot-line) hrs, respectively.

Journal: PLoS ONE

Article Title: Lys-315 at the Interfaces of Diagonal Subunits of δ-Crystallin Plays a Critical Role in the Reversibility of Folding and Subunit Assembly

doi: 10.1371/journal.pone.0145957

Figure Lengend Snippet: (A) Light scattering measurement. Monomeric K315A mutant δ-crystallin was incubated in 1.5 M urea before introducing varied GdmCl concentration. Refolding of 0.84, 3 and 5 M GdmCl denatured monomeric K315A mutant protein by dilution with 50 mM Tris-acetic acid buffer (pH7.5) or the buffer containing 1.5 M urea are shown as (●, ▲ and ■) or (○, ∆, and □), respectively. The label of (♦) represents refolding of 0.84 M GdmCl denatured monomers by dilution with buffer including αA-crystallin. αA-Crystallin alone in 1.5 M urea and 0.84 M GdmCl is shown as (◊). The protein concentrations of monomeric K315A and αA-crystallin used in the assays were 0.1 and 0.5 mg/mL, respectively. (B) The fluorescence spectrum of ThT were shown from refolding of 0.84 (dark), 3 (gray) and 5 M (dark gray) GdmCl denatured monomeric K315A mutant protein by dilution with buffer and incubated for zero (solid-line), 1 (dash-line) or 2 (dot-line) hrs, respectively.

Article Snippet: The structural model was used as a template to build the K315A mutant model using the build mutant protocol (Accelrys Discovery Studio 3.5, Accelrys Inc.).

Techniques: Mutagenesis, Incubation, Concentration Assay, Fluorescence

(A) The distances between the C α of specific residues located at the interfaces along the simulation. (B) The conformation of wild-type and K315A mutant protein at trajectory frame of 20 ps.

Journal: PLoS ONE

Article Title: Lys-315 at the Interfaces of Diagonal Subunits of δ-Crystallin Plays a Critical Role in the Reversibility of Folding and Subunit Assembly

doi: 10.1371/journal.pone.0145957

Figure Lengend Snippet: (A) The distances between the C α of specific residues located at the interfaces along the simulation. (B) The conformation of wild-type and K315A mutant protein at trajectory frame of 20 ps.

Article Snippet: The structural model was used as a template to build the K315A mutant model using the build mutant protocol (Accelrys Discovery Studio 3.5, Accelrys Inc.).

Techniques: Mutagenesis

The tetrameric wild-type (T) and K315A mutant (T*) δ-crystallin was dissociated through the diagonal dimer (D) and primary dimer (D*) to monomers with partial unfolded (M) and stable (M*) conformation, respectively. Monomers of the wild-type or the mutant protein were then denatured through intermediate (I or I*) into respective unfolded form (U or U*). The monomers (M) of wild-type protein in partial unfolded conformation was associated in alternative pathway to form dimers (D 1 ), and then assembled into tetramers (T 1 ) or aggregates (A). The aggregation was prevented by αA-crystallin. Refolding followed by assembly of the intermediates (I 1 * and I 2 *) of the mutant protein resulted in the aggregates (A 1 and A 2 ) formation and the chaperone function of αA-crystallin was invalid in this process.

Journal: PLoS ONE

Article Title: Lys-315 at the Interfaces of Diagonal Subunits of δ-Crystallin Plays a Critical Role in the Reversibility of Folding and Subunit Assembly

doi: 10.1371/journal.pone.0145957

Figure Lengend Snippet: The tetrameric wild-type (T) and K315A mutant (T*) δ-crystallin was dissociated through the diagonal dimer (D) and primary dimer (D*) to monomers with partial unfolded (M) and stable (M*) conformation, respectively. Monomers of the wild-type or the mutant protein were then denatured through intermediate (I or I*) into respective unfolded form (U or U*). The monomers (M) of wild-type protein in partial unfolded conformation was associated in alternative pathway to form dimers (D 1 ), and then assembled into tetramers (T 1 ) or aggregates (A). The aggregation was prevented by αA-crystallin. Refolding followed by assembly of the intermediates (I 1 * and I 2 *) of the mutant protein resulted in the aggregates (A 1 and A 2 ) formation and the chaperone function of αA-crystallin was invalid in this process.

Article Snippet: The structural model was used as a template to build the K315A mutant model using the build mutant protocol (Accelrys Discovery Studio 3.5, Accelrys Inc.).

Techniques: Mutagenesis

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