Premium
Cavities and packing at protein interfaces
Author(s) -
Hubbard Simon J.,
Argos Patrick
Publication year - 1994
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.5560031205
Subject(s) - solvation , polar , chemical physics , volume fraction , crystallography , protein subunit , protein structure , chemistry , hydrogen bond , protein domain , complementarity (molecular biology) , biophysics , physics , solvent , molecule , biology , biochemistry , organic chemistry , astronomy , gene , genetics
Abstract An analysis of internal packing defects or “cavities” (both empty and water‐containing) within protein structures has been undertaken and includes 3 cavity classes: within domains, between domains, and between protein subunits. We confirm several basic features common to all cavity types but also find a number of new characteristics, including those that distinguish the classes. The total cavity volume remains only a small fraction of the total protein volume and yet increases with protein size. Water‐filled “cavities” possess a more polar surface and are typically larger. Their constituent waters are necessary to satisfy the local hydrogen bonding potential. Cavity‐surrounding atoms are observed to be, on average, less flexible than their environments. Intersubunit and inter‐domain cavities are on average larger than the intradomain cavities, occupy a larger fraction of their resident surfaces, and are more frequently water‐filled. We observe increased cavity volume at domain‐domain interfaces involved with shear type domain motions. The significance of interfacial cavities upon subunit and domain shape complementarity and the protein docking problem, as well as in their structural and functional role in oligomeric proteins, will be discussed. The results concerning cavity size, polarity, solvation, general abundance, and residue type constituency should provide useful guidelines for protein modeling and design.