johngg@shiraz:~/perl/Monks$ perl -Mstrict -Mwarnings -E '
open my $inFH, q{<}, \ <<__EOD__ or die $!;
ProteinName    MF1    MF2    MF3
GH1    Growth factor activity    Growth hormone receptor binding    Hormone activity
POMC    G protein-coupled receptor binding    Hormone activity    Signaling receptor binding
THRAP3    ATP binding Source    Nuclear receptor transcription coactivator activity    Phosphoprotein binding 
__EOD__

chomp( my @lines = grep { ! m{^ProteinName} } <$inFH> );
close $inFH or die $!;

say join q{; }, split m{\s{2,}} for @lines;'
GH1; Growth factor activity; Growth hormone receptor binding; Hormone activity
POMC; G protein-coupled receptor binding; Hormone activity; Signaling receptor binding
THRAP3; ATP binding Source; Nuclear receptor transcription coactivator activity; Phosphoprotein binding