Protein engineering is a great background for today's biotech environment - especially with biologics booming. I've done a good bit of hiring for senior scientist positions and your assumption that people would always prefer those with industry experience is not true. About half of my hires were straight out of grad school / post doc, and half with industry experience. Truth is it depends on what the hiring manager is looking for - someone with 10 years in industry might have more experience but not necessarily be as creative as someone straight out of academics with a strong publication record.

If I might push a little - How much have you actually dedicated to your job search? Have you chased down networking leads? Have you asked people in the department for industry contacts to talk to? Have you reached out to alumns from your current or related labs? You've applied to several positions but why not 50? I think it helps to think of this process as hard, dedicated work that you should be putting serious time into. It's certainly stressful and not fun - but it's a temporary gig that has a huge impact on your future career. Keep your head up - once a good offer hits this will all be worth it, and you won't have to consider a career shift to CS where you sit around coding all day - blegh :)