Take the spaces out of $letters and you should get

$prot_object = bless( {
                        'primary_seq' => bless( {
                                                  'length' => 63,
                                                  '_root_verbose' => 0
+,
                                                  '_nowarnonempty' => 
+undef,
                                                  'seq' => 'MGPTSQPTLH
+PQNHAGIGLRKGKHLCVAYEPFLYLLLSQQGRKREEAAVERIRLREVGISLL*',
                                                  'alphabet' => 'prote
+in'
                                                }, 'Bio::PrimarySeq' )
+,
                        '_root_verbose' => 0
                      }, 'Bio::Seq' );
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whatever that means !