size and shape of protein molecules at the nanometer level determined by sedimentation, gel filtration, and electron microscopy蛋白质分子的大小和形状取决于沉积纳米水平,凝胶过滤,电子显微镜.pdf

Size and Shape of Protein Molecules at the Nanometer Level Determined by Sedimentation, Gel Filtration, and Electron Microscopy Harold P. Erickson Abstract An important part of characterizing any protein molecule is to determine its size and shape. Sedimentation and gel filtration are hydrodynamic techniques that can be used for this medium resolution structural anal- ysis. This review collects a number of simple calculations that are useful for thinking about protein struc- ture at the nanometer level. Readers are reminded that the Perrin equation is generally not a valid approach to determine the shape of proteins. Instead, a simple guideline is presented, based on the mea- sured sedimentation coefficient and a calculated maximum S, to estimate if a protein is globular or elon- gated. It is recalled that a gel filtration column fractionates proteins on the basis of their Stokes radius, not molecular weight. The molecular weight can be determined by combining gradient sedimentation and gel filtration, techniques available in most biochemistry laboratories, as originally proposed by Siegel and Monte. Finally, rotary shadowing and negative stain electron microscopy are powerful techniques for re- solving the size and shape of single protein molecules and complexes at the nanometer level. A combina- tion of hydrodynamics and electron microscopy is especially powerful. Keywords: Protein shape, hydrodynamics, gel filtration, sedimentation, electron microscopy. 1. Introduction Most proteins fold into globular domains. Protein folding is driv- en largely by the hydrophobic effect, which seeks to minimize contact of the polypeptide with solvent. Most proteins fold into globular domains, which have a minimal surface area. Peptides from 10 to 30 kDa typically fold into a single