You've got the idea! I'm not an HIV biologist, but typically these viruses utilize poly-cistronic transcripts. What that means is the proteins are made off the same mRNA so when they come off the ribosome they are local to the previous and next proteins being decoded. It's a very recurring theme in biology to have high _local_ concentration of things that you'd like to do a thing together.
Imagine a box of magnitiles that you just start throwing around the room. Well, instead of throwing them around the room and hoping they stick to each other, what if you only threw them around inside another box, which you were shaking vigorously? Well, you'd expect the magnitiles to find each other and stick to each other. Now imagine you attach each magnitile by a 1cm string and then throw them into a box and right after you through a string of 100 magnitiles, you start a new string of 100 magnitiles and throw that into the box instead of throwing it at the other side of the room.
The idea being concentration depends on the denominator of the volume you're in. If you have 2 things in a 1x1 meter box, you have a much higher concentration and therefore it is much more likely two things will bump into each other a lot than if you have 2 thing in a 1000 x 1000 meter box.
Also, a lot of these systems get made on the endoplasmic reticulum and so it then becomes a 2D search problem instead of a 3D search problem, reduces the volume of your box by an entire dimension! AND viruses tend to make little cordon off spots inside the cell where all their bits congregate, further increasing the chances they bump into each other the right way because, again, the _local_ concentration is super, super high.
Also keep in mind things at this scale bump into each other a mind boggling number of times per unit time. Like an asstillion number of times every second. Eventually they hit each other in the right way to stick together like magnitiles. They also vibrate constantly, which is called "exploring the conformational space". Anyway, I think you see my points.
Thank you for this, it really helped me visualise the process!
I find it amazing how the proteins not only have to create the shape in the end, but they also need to be able to snap together in the right conformation and avoid snaping together with other molecules that happen to be around there. And they must evolve that function in the first place. I intuitively have a hard time grasping what simple processes repeated an inumerable amount of time can produce in the end. And yet here we are.
Imagine a box of magnitiles that you just start throwing around the room. Well, instead of throwing them around the room and hoping they stick to each other, what if you only threw them around inside another box, which you were shaking vigorously? Well, you'd expect the magnitiles to find each other and stick to each other. Now imagine you attach each magnitile by a 1cm string and then throw them into a box and right after you through a string of 100 magnitiles, you start a new string of 100 magnitiles and throw that into the box instead of throwing it at the other side of the room.
The idea being concentration depends on the denominator of the volume you're in. If you have 2 things in a 1x1 meter box, you have a much higher concentration and therefore it is much more likely two things will bump into each other a lot than if you have 2 thing in a 1000 x 1000 meter box.
Also, a lot of these systems get made on the endoplasmic reticulum and so it then becomes a 2D search problem instead of a 3D search problem, reduces the volume of your box by an entire dimension! AND viruses tend to make little cordon off spots inside the cell where all their bits congregate, further increasing the chances they bump into each other the right way because, again, the _local_ concentration is super, super high.
Also keep in mind things at this scale bump into each other a mind boggling number of times per unit time. Like an asstillion number of times every second. Eventually they hit each other in the right way to stick together like magnitiles. They also vibrate constantly, which is called "exploring the conformational space". Anyway, I think you see my points.