Anabaena apoflavodoxin hydrogen exchange: On the stable exchange core of the alpha/beta(21345) flavodoxin-like family

An important issue in modern protein biophysics is whether structurally hom ologous proteins share common stability and/or folding features. Flavodoxin is an archetypal alpha/beta protein organized in three layers: a central b eta -sheet (strand order 21345) flanked by helices 1 and 5 on one side and helices 2, 3, and 4 on the opposite side. The backbone internal dynamics of the apoflavodoxin from Anabaena is analyzed here by the hydrogen exchange method. The hydrogen exchange rates indicate that 46 amide protons, distrib uted throughout the structure of apoflavodoxin, exchange relatively slowly at pH 7.0 (k(ex) < 10(-1) min(-1)). According to their distribution in the structure, protein stability is highest on the <beta>-sheet, helix 4, and o n the layer formed by helices 1 and 5, The exchange kinetics of Anabaena ap oflavodoxin was compared with those of the apoflavodoxin from Azotobacter, with which it shares a 48% sequence identity, and with Che Y and cutinase, two other alpha/beta (21345) proteins with no significant sequence homology with flavodoxins. Both similarities and differences are observed in the co res of these proteins. It is of interest that a cluster of a few structural ly equivalent residues in the central beta -strands and in helix 5 is commo n to the cores. Proteins 2001;43:476-488. (C) 2001 Wiley-Liss, Inc.