For reasons that aren't quite clear, there are two separate keyboard shortcuts for re-centering the protein.
The hotkey 'q' re-centers the protein and resets the fog and near/far visibility cutoffs. The hotkey 'Home' is similar, but also resets the zoom.
The 'q' hotkey actually has two modes. If you're hovering on the background, 'q' just re-centers the protein. If you're hovering over a segment, 'q' centers the view on that segment.
With 'q', the protein moves up, down, right, or left, but doesn't rotate.
'Home' always rotates the protein to a specific orientation, in addition to any other movement. 'Home' has only a single mode, and doesn't focus on a specific segment.
'Home' always been described as being "on Windows", but we've had hotkeys.txt for a while now. There's a key MISC_RECENTER_CAMERA in hotkeys.txt, that defaults to "Home".
Unfortunately, this mapping is not included in the "Configure Keyboard Shortcuts" dialog.
For anyone with a keyboard lacking the 'Home' key, it should be possible to edit hotkeys.txt while Foldit is not running. Find MISC_RECENTER_CAMERA and change "Home" to an unused combination, like "Alt+C". Save the file, and start Foldit. With a little luck, the "re-center camera" will now be available.
If you do make this change, be sure to add hotkeys.txt to the list containing all.macro and maybe options.txt and theme.txt as key files. It's good to have a recent backup of these files at least in case Something Bad Happens.
If Galileo were here, he'd insist that I mention that the protein is actually not what's moving. Instead, we're looking through a camera that moves in space. The protein can move in space if you pull on it or wiggle it, but for 'q' and 'Home', protein stays put.