Hi,
I can't reproduce the problem. All works well for me:

C:\_32\pscrpt>type fragment.txt
Hello Workload !!
More stuff

C:\_32\pscrpt>type try.pl
#!/usr/bin/perl -w

$proteinfilename = 'fragment.txt';
open(PROTEINFILE, $proteinfilename);
$protein = <PROTEINFILE>;
close PROTEINFILE;
print " here is the protein:\n\n";
print $protein;

C:\_32\pscrpt>perl try.pl
 here is the protein:

Hello Workload !!

C:\_32\pscrpt>
[download]

As you can see, your script outputs only the first line of fragment.txt.

Cheers,
Rob