dilute NaOH causes hydrolysis

[Reno T. Nguyen]

I've been extracting proteins from various matrices (e.g., algae and
sediments) using 0.5 N NaOH and then estimating total protein by a
colorimetric assay.  This method seems to work well, as long as the
standards are treated the same way. NaOH has been used by other
researchers for extraction of sedimentary protein. 

I was hoping to analyze the MW distribution of proteins extracted as
described above. After buffering to a pH of 6.8, I used one of Millipore's
ultrafiltration devices to concentrate the proteins; diluted the salts
using buffer; ran SDS-PAGE.  None of the protein standards (e.g., BSA)
were observed in the correct MW range.  However, I did notice a smear in
the low MW range suggesting protein hydrolysis. 

I'm aware that 2 to 4 N NaOH (at 100 deg C for 4 to 8 h) will normally
hydrolyze proteins completely. Would a NaOH concentration as low as 0.5 N
hydrolyze proteins to some extent, even if the samples are extracted at
room temperature instead of 100 deg C?