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. Author manuscript; available in PMC: 2017 Aug 25.
Published in final edited form as: J Phys Chem B. 2016 Apr 6;120(33):8137–8146. doi: 10.1021/acs.jpcb.6b01327

Figure 2.

Figure 2

Properties of the flexible arm of human Rpn10. A. The starting structure (left) and a representative structure (right) of an Rpn10 fragment from MD simulations. Amino acids marked in red are negatively charged, blue are positively charged, orange are hydrophobic, black comprise UIM1, and grey cover the rest. B. Interacting nonpolar residues/groups of Rpn10 fragment; the structure is the same as in panel A (right). C. Percentage of time residue pairs (respective residues represented by their center-of-mass) shown in panel B remained within 7 Å of each other. D. Electrostatic properties of the Rpn10 fragment with protected UIM1. E. Electrostatic properties of Rpn10 fragment without protected UIM1 (reported earlier6). The surface of the fragment is colored according to the color bar with electrostatic energy given in units of kBT/e, where kB is Boltzmann's constant, T is the temperature, and e is the charge of an electron. F. Aligned sequences of Rpn10 flexible arms. The color code is the same as in panel A. Note: in panel A, B, D, and E, residues 196-244 of Rpn10 are shown. The alignment of the full sequences is provided in Fig. S2.