Are proteins a different shape in space?
Proteins are not made to be one way up or the other as they flow around and surround cells, so sea-level to space gravity gradient will not be the major cause of change to proteins at different altitudes.

Pressure is more of a factor on proteins, and it has been studies very much, both for protein shape and protein interaction with elements and other molecules.

http://www.annualreviews.org/doi/abs/10.1146/annurev.pc.44.100193.000513?journalCode=physchem

People have awesome health when they are born and raised at altitudes of 4000 meters, there are even people living at 4800 meters OK. the pressure gradient there is halfway in between sea level and space. 100m depth also stresses nitrogen toxicity and other severe effects more than proteins, but deep sea fish do have specially adapted proteins because depths at 10000 meters require different proteins than the surface.