Energy hole problem is a critical issue for data gathering in wireless sensor networks. Sensors near the static sink act as relays for far sensors and thus will deplete their energy very quickly, resulting energy holes in the sensor field. Exploiting the mobility of a sink has been widely accepted as an efficient way to alleviate this problem. However, determining an optimal moving trajectory for a mobile sink is a non-deterministic polynomial-time hard problem. Thus, this paper proposed a mobile sink-based adaptive immune energy-efficient clustering protocol (MSIEEP) to alleviate the energy holes. A MSIEEP uses the adaptive immune algorithm (AIA) to guide the mobile sink-based on minimizing the total dissipated energy in communication and overhead control packets. Moreover, AIA is used to find the optimum number of cluster heads (CHs) to improve the lifetime and stability period of the network. The performance of MSIEEP is compared with the previously published protocols; namely, low-energy adaptive clustering hierarchy (LEACH), genetic algorithm-based LEACH, amend LEACH, rendezvous, and mobile sink improved energy-efficient PEGASIS-based routing protocol using MATLAB. Simulation results show that MSIEEP is more reliable and energy efficient as compared with other protocols. Furthermore, it improves the lifetime, the stability, and the instability periods over the previous protocols, because it always selects CHs from high-energy nodes. Moreover, the mobile sink increases the ability of the proposed protocol to deliver packets to the destination.