In early 1951 Pauling became so engrossed in his protein structure research that he began devoting less time to politics. Regardless, in April, HUAC named him among the foremost Americans involved in what the committee called a "Campaign to Disarm and Defeat the United States." The publicity resulted in two colleges withdrawing invitations for Pauling to speak. That same spring, the war in Korea deepened, the Rosenbergs went on trial for espionage, and Truman expanded his loyalty program. In July, Pauling was again scheduled to appear before an investigatory committee, this time for a hearing after a routine application for a low-level security clearance -- something he had been granted since World War II -- was denied. Pauling’s two days of testimony before the board again resulted in headlines linking the Caltech scientist to any number of questionable groups and activities. Then it was discovered that the security clearance snafu had been the result of an administrative error; the latest investigation need never have been made.

Still, the damage had been done, both to Caltech, whose President was now beginning to tire of Pauling’s ceaseless activism, and to Pauling himself. His science was going extremely well, with his breakthrough protein papers generating some of the highest praise he had ever received. Now, finally, he seemed to decide that it was better to pull back from his political work. After a long talk with Ava Helen, two days after the security clearance hearing ended he sent letters of resignation to the American Association of Scientific Workers and the National Council of the Arts, Sciences, and Professions, two groups often cited as Communist-dominated. He told another suspect group that he could not serve as an officer. Within a few months he also resigned from the World Federation of Scientific Workers, an international group headed by a distinguished French researcher who also happened to be a Communist, writing that he was "too busy" to give the group proper attention.

Through the remainder of 1951 and 1952, Pauling did not give a single strictly political talk, shied away from giving political statements to the press, and refused to join any group identified as pro-Communist. He concentrated on science. But even here, politics followed him. The State Department in the spring of 1952 refused to issue Pauling a passport to travel to England to discuss his protein ideas, writing that his proposed trip "would not be in the best interests of the United States." He was, in effect, being held within the United States. A combination of press scrutiny and public concern convinced the State Department to back down and, some months later, reinstate Pauling’s passport.