User:Ruwan23

"Sequential Model" Review by Isaiah Herrera

Overall, the article was organized logically and the history went into appropriate depth of this model’s creation. I was impressed by the section that made a clear comparison between the Monod-Wyman-Changeux model and the sequential model. I would suggest adding specific examples of proteins that exhibit this model. In particular, images using Pymol would allow for a better look into the 3D structural changes that are described in this method. I would also move the section “Comparison to the MWC Model” earlier in the article since reference to the MWC model is constant throughout the entirety of the article. This article should start with the sequential model’s place in the overall scheme of protein modeling. The article left me with broad questions about different models and it would be nice if there was a list of different models that have been developed in the past or are currently developing in the beginning of the article. Could binding of ligand induce a mixture of negative cooperatively and positive cooperatively using this model? What happens if a protein does not follow the i³ nature? Could this model or another model be applied to this situation? 

Positive cooperativity increases an enzyme's responsiveness to ligand binding, thus amplifying a biological signal.^[1]

Negative cooperativity is better understood in the KNF, or sequential, model, where binding of one subunit can reduce the binding affinity of the next subunit for the same ligand. Conversely, the MWC model allows only for positive cooperativity, as ligand binding cannot further stabilize the T, or low-affinity, state. It can only increase affinity, as the enzyme switches from the T to the R state.^[2]Proteins that exhibit negative cooperativity can thus be modeled by the KNF model.^[3]

Experiments involving non-cooperative and cooperative competitive ligand binding has illustrated that the KNF model is able to account for mixed cooperativity, or greater negative or positive cooperativity at different locations in the binding curve.^[4]

Outline

1. History
   1. MWC model
   2. emergence of KNF model by Koshland et al.
2. Rules guiding the KNF model
   1. induced-fit model: change in conformation of enzyme to improve binding affinity to transition state, catalyzing reaction
   2. KNF model is conducive to this, where each ligand binding site changes affinity to the ligand, or the transition state of the ligand in the case of catalysis
3. Comparison to the MWC model
   1. KNF predicts negative and mixed cooperativity, not possible with the MWC model
   2. T and R state vs. induced fit
4. Adherence to Biochemical Data
   1. Hemoglobin by the MWC model
   2. hemoglobin by the KNF model

1. https://en.wikipedia.org/wiki/Sequential_model
2. http://bio.libretexts.org/Core/Biochemistry/Binding/MODEL_BINDING_SYSTEMS#Free_Energy_and_Cooperativity^[1]
3. Tertiary and quaternary effects in the allosteric regulation of animal hemoglobins.^[5]
4. Structure and Mechanism in Protein Science^[2]
5. Ligand Competition Curves as a Diagnostic Tool for Delineating the Nature of Site-Site Interactions : Theory^[4]
6. Proteomics and Models for Enzyme Cooperativity^[3]