( ( ( Protons and ) neutrons ) ( ( ( ( are ( in ( ( the center ) ( of ( the atom ) ) ) ) ) , ) ( ( making up ) ( the nucleus ) ) ) . ) )
(ROOT (S (NP (NNS Protons) (CC and) (NNS neutrons)) (VP (VBP are) (PP (IN in) (NP (NP (DT the) (NN center)) (PP (IN of) (NP (DT the) (NN atom))))) (, ,) (S (VP (VBG making) (PRT (RP up)) (NP (DT the) (NN nucleus))))) (. .)))
Protons and neutrons are in the center of the atom, making up the nucleus.
(ROOT (S (NP (NP (DT The) (NN atom)) (PP (IN in) (NP (DT a) (NN neutron)))) (VP (VBZ is) (VP (VBN found) (PP (IN in) (NP (DT the) (DT the) (NN nucleus))))) (. .)))