( ( ( Protons and ) neutrons ) ( ( are ( in ( ( ( the center ) ( -LRB- ( nucleus -RRB- ) ) ) ( of ( the atom ) ) ) ) ) . ) )
(ROOT (S (NP (NNS Protons) (CC and) (NNS neutrons)) (VP (VBP are) (PP (IN in) (NP (NP (NP (DT the) (NN center)) (PRN (-LRB- -LRB-) (NP (NN nucleus)) (-RRB- -RRB-))) (PP (IN of) (NP (DT the) (NN atom)))))) (. .)))
Protons and neutrons are in the center (nucleus) of the atom.
(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))))) (. .)))