7: Binding
- Page ID
- 150318
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)- 7.3: Model Binding Systems
- C1. Myoglobin, Hemoglobin, and their Ligands
- C10. Macromolecule Oligomer Formation and Symmetry
- C11. Conformational and Binding - Examples
- C12. Free Energy and Cooperativity
- C13. Links and References
- C2. Normal and Cooperative Binding of Dioxygen
- C3. Mathematical Analysis of Cooperative Binding - Hill Plot
- C4. Mathematical Analysis of Cooperative Binding - MWC Symmetry Model
- C5. Mathematical Analysis of Cooperative Binding - KNF Sequential Model
- C6. Conformational Selection
- C7. Binding to Intrinsically Disorder Protein and MORFs
- C8. Binding, Intracellular Granules and Droplets
- C9. Binding and Linked Equilibria
- 7.4: Binding and the Control of Gene Transcription
- One of the central questions of modern biology is what controls gene expression. As we have previously described, genes must be "turned on" at the right time, in the right cell. To a first approximation, all the cells in an organism contain the same DNA (with the exception of germ cells and immune cells). Cell type is determined by what genes are expressed at a given time. Likewise, cells can change (differentiate) into different types of cells by altering the expression of genes.
- D1. Introduction to Transcription
- D10. Epigenetic Control of DNA - Methylation
- D11. Chromatin Remodeling and Gene Expression
- D12. Acetylation and Methylation of Histones
- D13. Control of Gene Expression by RNA
- D14. Recognition of viral and bacterial DNA by the immune system
- D16. Eukaryotic Species Complexity
- D17. Gene Expression Differences Between Humans and Chimpanzees
- D18. Links and References
- D2. Control of Transcription in Prokaryotes
- D3. Control of Gene Transcription in Eukaryotes
- D4. DNA Binding Sites
- D5. DNA Binding Proteins
- D6. Studying the Interactome
- D7. Phosphorylation and Control of Gene Expression
- D8. Classification of Transcription Factors
- D9. Cooperative Binding of Proteins to DNA
- Encyclopedia of DNA Elements
- 7.5: New Methods in Drug Development
- E1. Introduction to Drug Development
- E10. Diseases of Protein Misfolding and Aggregation
- E11. Links and References
- E2. Combinatorial Drug Development
- E3. Computer Design of Drugs
- E4. In Situ Click Chemistry in Drug Synthesis
- E5. DNA Binding Drugs
- E6. DNA Binding and Genomic Analyses
- E7. RNA Binding Drugs
- E8. Multivalent Inhibitors
- E9. Targeted Delivery of Drugs to Tumors
- 7.6: 5F. Immune System Recognition
- In this last chapter on binding, we will consider the daunting task faced by the immune system - to recognize all possible "foreign" molecules and react to them, either by targeting them for elimination, or, paradoxically, to recognize them but not react to them (a process called tolerance). The same can be said of "self-molecules". The immune system must recognize them but not respond to them, otherwise autoimmune disease might arise in which the body's powerful immune system targets self.
Thumbnail: C/EBPα bZip domain bound to DNA. PDB entry 1nwq. Image used with permission (CC BY-SA 3.0; A2-33).