Aided by its cofactor, pyridoxal phosphate, NFS1 supplies sulfur by removing it from cysteine residues, and ISCU provides the backbone structure and the cysteine ligands upon which a new cluster consisting of covalently bound iron and inorganic sulfur is synthesized (Raulfs et al., 2008; Py and Barras, 2010; Bandyopadhyay et al., 2008; Lill, 2009).
In the crystalline state, the peptide backbone structures and the side-chain conformations at Tyr-3, Tyr-5, and Tyr-6 of this analogue and of RA-II were very similar.
To analyze the thermal stability of the polyester hydrolases, the time course of the root-mean-square deviation (RMSD) of backbone structures and the root-mean-square fluctuation (RMSF) of Cα atoms of each amino acid residue over the complete 50 ns simulation were calculated using GROMACS 4.6 (Hess et al. [2008]).
The distinct sequences of the partners do not adopt identical backbone structures, and the various side chain interactions between 14-3-3 14-3-3 14-3-3ifferent pandners involve induced-fithedjustwonts of the 14-3-3 structure.
To address this, we compared the predicted side-chain structures given the native backbone structures and those given the predicted backbone structures in terms of free energy.
If a species tree is provided in addition to the collection of gene trees, our algorithm considers it as the dominant evolutionary history (i.e., backbone structure) and uses the collection of gene trees to infer the most significant reticulation events.
Moreover, the crystal structure of the synaptotagmin-7 C2B domain described here shows that its backbone structure and even the conformations of many side chains are very similar to those of the synaptotagmin-1 C2B domain, suggesting that their functional differences do not arise from distinct structural properties.
First, we solve the protein structure idealization problem by idealizing the backbone structure and then idealizing the side-chain structure.
The Cry8Ka1 and Cry8Ka5 mutant models had the same backbone structure and differed only in the mutated side chains.
This class of drugs (artemisinins) contains an intramolecular peroxide bridge that is situated in the sesquiterpene lactone backbone structure and is key to the antimalarial function [4].
In addition, with the introduction of a positively charged lysine residue, the carboxyl groups of two Asp residues are being forced to come closer together (Fig. 3a and b), which might create tension in the protein backbone structure and trigger certain conformational changes in the Apaf-1 protein.
