What I wonder is that assuming I have two proteins namely protein-A, protein-B and protein A is somehow modified by protein B (simply an enzyme catalyzing the addition of -OH group to certain Proline residues in protein-A), is it feasible to acquire profound insight as to how the protein-B comes closer to the certain sites in the protein-A and initiate the interaction?. More broadly can one be able to investigate how the structure of an enzyme affect what it does in a dynamic way (conformational changes along the catalysis, how the rest of the enzyme rather than the active sites contributes to its function or any important water enzyme interaction etc.). And besides that how one should think of the catalysis process in an intuitive way. What I mean by that is in biochemistry books it is just said that "This enzyme adds Oxygen from the dioxygen in the environment....." I mean how should one imagine this process in a more physical and theoretical way ?. It really bothers me the fact that I just cannot imagine the cascade of events in a more scientific and theoretical manner. Also if these questions are so trivial forgive my ignorance on the matter. Any suggestion would be much appreciated, thanks in advance.
Imagine protein A and protein B in aqueous solution. Each is surrounded by water molecules, but more importantly, each has a solvation shell (in this case, hydration shell) around it. There are several layers of these hydration shells (HS). The first HS is more tightly bound to the protein than the 2nd layer, and the 3rd layer more loosely bound than the 2nd layer, and so on, until you reach the bulk solvent which is no longer bound to the protein. Now recall Brownian motion and Collision Theory in solution. Protein A and protein B not only needs to encounter each other; for them to get in direct contact with each other, they each have to overcome their respective HSs, but also be in the precise orientation with respect to each other so that their reactive centers (which are specific in both proteins) are in close proximity. Only then can protein B do its job of adding -OH to protein A. So not all encounters between A and B are fruitful. I hope this short scenario helps you imagine the "cascade of event" (as you said) that lead to the reaction between proteins A and B. (NOTE: Protein B must somehow pick up a water molecule in the vicinity and transfer its -OH to a proline residue in protein A -- I missed including this step in the above scenario, but you do get the point).
Imagine protein A and protein B in aqueous solution. Each is surrounded by water molecules, but more importantly, each has a solvation shell (in this case, hydration shell) around it. There are several layers of these hydration shells (HS). The first HS is more tightly bound to the protein than the 2nd layer, and the 3rd layer more loosely bound than the 2nd layer, and so on, until you reach the bulk solvent which is no longer bound to the protein. Now recall Brownian motion and Collision Theory in solution. Protein A and protein B not only needs to encounter each other; for them to get in direct contact with each other, they each have to overcome their respective HSs, but also be in the precise orientation with respect to each other so that their reactive centers (which are specific in both proteins) are in close proximity. Only then can protein B do its job of adding -OH to protein A. So not all encounters between A and B are fruitful. I hope this short scenario helps you imagine the "cascade of event" (as you said) that lead to the reaction between proteins A and B. (NOTE: Protein B must somehow pick up a water molecule in the vicinity and transfer its -OH to a proline residue in protein A -- I missed including this step in the above scenario, but you do get the point).
First of all, thank you a lot for your attention and detailed explanation on the matter. "Protein B must somehow pick up a water molecule in the vicinity and transfer its -OH to a proline residue in protein A", that is what I thought too. So can I assume that some of the residues in the protein B will attract water molecules due to electrostatic interactions or shortly via non-covalent interactions and along the arrangement of the optimum orientations of both proteins this specific water molecule will move with the protein B or somehow during the arrangement of orientation new, more suitable water molecule will go and move with the protein B so and so forth till the best geometrical arrangement is reached. How can we express the term "transfer" from chemistry perspective ?.
The mechanism of -OH transfer either from a water molecule in the bulk solvent or a specific one pre-bound in the active site of the enzyme may be the information that your MD simulation might reveal.
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