Use the zip command:

zip -e -r "name_of_the_new_zip_file" "path_of_the_folder_which_has_to_be_protected"

Example:

If you want to protect a folder named "old" in your desktop. Just do it...

zip -e -r /home/gautam/Desktop/new /home/gautam/Desktop/old

[gautam@gautam-home ~]$ zip -e -r /home/gautam/Desktop/new /home/gautam/Desktop/old
Enter password:
Verify password:

This will create a zip file named "new.zip" in your desktop (new.zip). After that delete the folder "old".