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I know that the sum of the mass of the two proton is greater than the mass of a helium nucleus (two proton). As the mass different is transformed into energy by the Einstein mass energy-equivalence. If the gravity is related with mass, then the gravitational force given by the helium nucleus will be less then the sum of the gravitational force given by the two proton separately. And if it is so, then what is the actual source of gravity?

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A helium nucleus is not two protons, it is two protons and two neutrons. Instead you can compare two deuterium nuclei (one proton and one neutron) with one helium nucleus, so you have the same number of nucleons of the same types.

And the answer is (as far as I am aware): no, there is no experimental evidence for the magnitude gravitational forces produced by individual nucleons. The forces involved are far, far, far, far too small for us to measure them, and the predicted difference between them due to binding energy is even smaller still.

Don't forget that gravitational forces are about $10^{14}$ times weaker than electromagnetic forces, so you'd need to be able to account for electromagentic forces with better than 14 significant figures of precision before you could hope to have any chance of directly measuring the gravitational forces.

Gravity can be measured at large scales simply because it is always attractive, while EM forces tend to cancel out, so as you add more and more mass into consideration, the net charge remains very close to zero while the gravitational forces just get bigger and bigger. But if you are dealing with large enough masses of helium and deuterium to be able to measure gravitational effects plausibly, do you actually know the number of nuclei of each that you have precisely enough? Nope.

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