TATA-Binding Protein Mutants
Calculation of biochemical reaction pathways taking into account oncogenic mutations and gene expression.
Familiarize yourself with the main list of calculations.
Step-by-step approaches in checking the correctness of building X-ray structures (PDB files)
Biomarker development concept
Symbol: TBP
Name: TATA box binding protein
Synonyms: GTF2D1
SCA17
TFIID
Name: TATA box binding protein
Synonyms: GTF2D1
SCA17
TFIID
Calculation of biochemical pathways of biochemical reactions taking into account oncogenic mutations and gene expression.
Cryo-EM structures of TFIID and its binding to DNA.
- Recent insights into the structure of TFIID, its assembly, and its binding to core promoter// Published in final edited form as:
TAF1 (TATA-Box Binding Protein Associated Factor 1) is a Protein Coding gene. Diseases associated with TAF1 include Intellectual Developmental Disorder, X-Linked, Syndromic 33 and Dystonia 3, Torsion, X-Linked.
Human TAF2 (originally called either CIF150 or TAFII150) has been previously described as an essential cofactor for TFIID-dependent transcription from promoters with initiator (Inr)-containing promoter elements. A trimeric TBP–TAF1–TAF2 complex is minimally required for efficient utilization of the Inr and downstream promoter elements
TAF9 was reported to be a crucial P53 coactivator for the stabilization and activation of P53. TAF9 inhibits the MDM2-mediated degradation of p53 by reducing MDM2 binding to p53. One TFIID complex lacking TAF9 in Hela cells causes apoptosis. The interruption of interactions between Hedgehog transcription factors (Gli proteins) and TAF9 reduces Gli/TAF9-dependent transcription, suppresses cancer cell proliferation, and reduces xenograft growth
Human TAF8 is a 310 amino acid protein harboring a histone fold domain (HFD) at its N-terminal end, which interacts with the HFD of TAF10, to form a noncanonical histone fold pair arrangement in TFIID TAF8 also interacts with TAF2 and TAF2-TAF8-TAF10 subcomplex assembles in the cytoplasm of human cells. Biochemical studies revealed that TFIID is assembled in a stepwise manner, first forming a stable 5TAF core complex, consisting of two copies each of TAF5-TAF6-TAF9-TAF4-TAF12.
Symbol: GTF2F2
Name: general transcription factor IIF, polypeptide 2, 30kDa
Synonyms: BTF4
RAP30
TFIIF
Name: general transcription factor IIF, polypeptide 2, 30kDa
Synonyms: BTF4
RAP30
TFIIF
Symbol GTF2B
Name general transcription factor IIB
Synonyms TFIIB
Name general transcription factor IIB
Synonyms TFIIB
Symbol: GTF2A2
Name: general transcription factor IIA, 2, 12kDa
Synonyms: HsT18745
TFIIA
Name: general transcription factor IIA, 2, 12kDa
Synonyms: HsT18745
TFIIA
Structure
Structure of TBP and DNA showing some gene mutations in various oncological diseases
Most Frequent Somatic Mutations
Structure
Structure of TFIIB and DNA showing some gene mutations in various oncological diseases
Most Frequent Somatic Mutations
Structure
Structure of TFIIF and DNA showing some gene mutations in various oncological diseases
Most Frequent Somatic Mutations
Most Frequent Somatic Mutations
Structure
Structure of TFIIF and DNA showing some gene mutations in various oncological diseases
Ways of biochemical reactions taking into account various oncological mutations, examples and calculations of various biochemical complexes
A
1
1
2
4
4
5
5
TBP
DNA
TFIIB
TFIIA
4
a) Scheme of changes in resistance with various substitutions in TF2B when bound to DNA
b) Structure of the complex of DNA and TF2B
b) Structure of the complex of DNA and TF2B
1
3
Structure of the complex of DNA, TF2B and TFIIA
5
B
Calculation and Data Analysis
Calculation and Data Analysis
The experimental data are compared with the calculated data
Initial stage.
Comparison of calculated and experimental data.
Comparison of calculated and experimental data.
Verification of calculated and experimental data before conducting a large-scale computational process
The effect of the R188E is a direct effect on DNA binding by the TBPCORE
Figure 1. Wild-Type and Activated DNA Binding Mutant TBP Molecules Have Different TATA Box On Rates and Different DNA Binding Surfaces. Electrophoretic mobility retardation analyses of the rates of formation of the TBP-TATA box complex on the U6 promoter with (A) wild-type TBP and the (B) TBPR188E mutant TBP molecules.
A master binding reaction was prepared at 30C, and aliquots were removed at 1, 4, 9, 16, 25, 36, 49, 64, 81, and 100 min and immediately loaded onto the gel.
A master binding reaction was prepared at 30C, and aliquots were removed at 1, 4, 9, 16, 25, 36, 49, 64, 81, and 100 min and immediately loaded onto the gel.
After incubation of a master binding reaction for 100 min at 30C, excess unlabeled DNA was added, and aliquots werremoved after an additional 1, 4, 9, 16, 25, 36, 49, 64, 81, and 100 min incubation at 30C and immediately loaded onto the gel. The graphs below the autoradiograms show the dissociation of TBP from the TBP-TATA box complexes over incubation time after addition of the competitor DNA. The unit of the vertical axis is arbitrary. Filled dots and open triangles represent the unbent TBPFL and bent TBPFL* complexes respectively.
Figure 2. The Bent, But Not the Unbent, Wild-Type TBP-TATA Box Complex Is Very Stable. Electrophoretic mobility retardation analysis of the dissociation rates of (A) TBPWT and (B) TBPR188E molecules from the TBP-TATA box complexes on the U6 promoter.
TBPR188E formed a TBPFL* complex rapidly beginning within 1 min of incubation and formation of the complex increased rapidly with timenot simpler.
C
lg(cond(W))_______Kd
the calculated stability value lg(cond(W)) is qualitatively proportional to the experimental value Kd
An additional controlled parameter is the measure of change in the differential entropy (delta)H
The results of numerical calculations.
Conclusions from the experimental results are shown above the graph, agreement is indicated by arrows
Conclusions from the experimental results are shown above the graph, agreement is indicated by arrows
neither alanine nor radical
mutations showed any activated DNA binding activity.[1]
mutations showed any activated DNA binding activity.[1]
radical mutations showed activated TBPFL* DNA binding, although the radical mutations were more active.[1]
the radical but not alanine mutations activated formation of
the TBPFL* complex[1]
the TBPFL* complex[1]
- A Regulated Two-Step Mechanism of TBP Binding to DNA: A Solvent-Exposed Surface of TBP Inhibits TATA Box Recognition
Xuemei Zhao and Winship Herr
Cold Spring Harbor Laboratory
Cold Spring Harbor, New York 11724
In the standard 30 min incubation, residues are either inactive or only form the TBPFL complex for both alanine and radical substitutions: L185(A and K), E191(K), R203(A and E), E206(A and K), R208(A and E)[1]
D
decrease in stability
DNA-TBP binding
DNA-TBP binding
increased in stability
increased in stability
increased in stability
DNA-TBP binding
DNA-TBP binding
decrease in stability
The Cancer Genome Atlas analysis.
The Cancer Genome Atlas analysis.
Symbol: TBP
Name: TATA box binding protein
Synonyms: GTF2D1
SCA17
TFIID
Name: TATA box binding protein
Synonyms: GTF2D1
SCA17
TFIID
Symbol: GTF2B
Name: general transcription factor IIB
Synonyms: TFIIB
Name: general transcription factor IIB
Synonyms: TFIIB
Symbol: GTF2A2
Name: general transcription factor IIA, 2,
Synonyms: HsT18745
TFIIA
Name: general transcription factor IIA, 2,
Synonyms: HsT18745
TFIIA
Ниже приведены описание и перечень таких мутаций для выбранных белков TBP, GTF2B, GTF2A, для которых будет выполнен расчет связывания c учетом различных мутаций в белках, взятых из Cancer Genome Atlas.
- Choose a mutation.
- Choose a biochemical reaction.
- Get Information
Determine the effect of each of the mutations on the course of biochemical reactions.
E
Symbol: GTF2B
Name: general transcription factor IIB
Synonyms: TFIIB.
Name: general transcription factor IIB
Synonyms: TFIIB.
Each molecular complex is characterized by its stability value lg(cond(W)), while the formation of each complex is characterized by its forward and reverse chemical reaction constants Kn and K-n
TFIIB
TBP
DNA
4.6375_________ _____5.265e-19___________ 1.213e-23______ 6.266e-32
[TFIIB-TBP-DNA]
__number ___________________ max _________________min _________________error condition__________________________________________________________computational SVD
4.681____________________5.929e-19_________1.235e-23___________5.191e-19
__number ___________________ max _________________min _________________error condition__________________________________________________________computational SVD
Symbol: TBP
Name: TATA box binding protein
Synonyms: GTF2D1
SCA17
Name: TATA box binding protein
Synonyms: GTF2D1
SCA17
2.643____________5.1678e-19______________1.174e-21____________6.478e-32
__number ___________________ max _________________min _________________error condition__________________________________________________________computational SVD
F
GTF2A2
CH3
Figure 1. Structure of CH3-GTF2A2 dimer
Figure 2. Structure of biological complex
[TBP-DNA-TFIIB-THIIA-CH3]
[TBP-DNA-TFIIB-THIIA-CH3]
Figure 3.Calculation results for various structures in which various substitutions of amino acid residues were introduced.
Figure 4. Calculation results for various structures in which various substitutions of amino acid residues were introduced.
Calculation results for various dimer structures and four proteins associated with DNA, in which various amino acid residue substitutions were introduced.
G
