in vivo的蛋白质研究常常专注于蛋白质在细胞中的合成和定位。虽然已经知道许多细胞内蛋白质是在细胞质中合成,而膜结合蛋白质或分泌性蛋白质是在内质网中合成,但蛋白质定位到特定细胞器或细胞结构的特异性是如何达到的,目前还不清楚。一些有助于获得特定蛋白质在细胞中定位的方法得到了发展,特别是用基因工程将目的蛋白质上连接上“报告者”(如绿色荧光蛋白),将这样的融合蛋白在细胞中表达后,就可以通过显微镜观察荧光来了解融合蛋白在细胞中的分布。[25]
对于早期的生物化学家来说,研究蛋白质的困难在于难以纯化大量的蛋白质以用于研究。因此,早期的研究工作集中于能够容易地纯化的蛋白质,如血液、蛋清、各种毒素中的蛋白质以及消化性和代谢酶(获取自屠宰场)。1950年代后期,Armour Hot Dog公司纯化了一公斤纯的牛胰腺中的核糖核酸酶A(英语:Ribonuclease A),并免费提供给全世界科学家使用。目前,科学家可以从生物公司购买越来越多的各类纯蛋白质。
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