Refined solution structure and backbone dynamics of the archaeal MC1 protein

Abstract

The 3D structure of methanogen chromosomal protein 1 (MC1), determined with heteronuclear NMR methods, agrees with its function in terms of the shape and nature of the binding surface, whereas the 3D structure determined with homonuclear NMR does not. The structure features five loops, which show a large distribution in the ensemble of 3D structures. Evidence for the fact that this distribution signifies internal mobility on the nanosecond time scale was provided by using 15N‐relaxation and molecular dynamics simulations. Structural variations of the arm (11 residues) induced large shape anisotropy variations on the nanosecond time scale that ruled out the use of the model‐free formalism to analyze the relaxation data. The backbone dynamics analysis of MC1 was achieved by comparison with 20 ns molecular dynamics trajectories. Two β‐bulges showed that hydrogen bond formation correlated with ϕ and ψ dihedral angle transitions. These jumps were observed on the nanosecond time scale, in agreement with a large decrease in 15N‐NOE for Gly17 and Ile89. One water molecule bridging NH(Glu87) and CO(Val57) through hydrogen bonding contributed to these dynamics. Nanosecond slow motions observed in loops LP3 (35–42) and LP5 (67–77) reflected the lack of stable hydrogen bonds, whereas the other loops, LP1 (10–14), LP2 (22–24), and LP4 (50–53), were stabilized by several hydrogen bonds. Dynamics are often directly related to function. Our data strongly suggest that residues belonging to the flexible regions of MC1 could be involved in the interaction with DNA.

Initial Insights into Structure-Activity Relationships of Avian Defensins

“…1), the Gly-Xaa-Cys and Cys-Cys-positive motifs are replaced by Gly-Xaa-Xaa-Cys and "Cys-Cys-Xaa-positive," respectively ( Fig. 1), (42), and/or it could give flexibility to this part of the protein (43). It is noticeable that this bulge is present in all the mammal ␤-defensin three-dimensional structures presently known: human hBD1-6, bovine BD12, and mouse mBD7-8 (Protein Data Bank codes 1kj5, 1fd3, 1kj6, 1zmm, 1zmp, 1zmq, 1bnb, 1e4t, and 1e4r, respectively).…”

Model of a DNA-Protein Complex of the Architectural Monomeric Protein MC1 from Euryarchaea

“…The free protein NMR sample was prepared by concentrating 15 N-MC1 to 1.6 mM (10 mM phosphate buffer pH 6, 100 mM NaCl, 1 mM EDTA, 10% D 2 O) as described previously [9].…”

“…The 15 N and 1 H N chemical shifts for free MC1 have already been reported [9] and those for bound MC1 were assigned from a combination of 1 H- 15 N HSQC (heteronuclear single quantum coherence) and 2D 15 N NOESY-HSQC (mixing time of 150 ms) spectra. Chemical shift perturbation (CSP) data of the protein were calculated and analyzed with SAMPLEX [18].…”

“…R 2 for the diamagnetic state was given previously [9] and R 2 for the paramagnetic state was measured with R 2 relaxation delays of 2, 3, 4, 5, 6, 7, 8, 10, 12, 14, 16, 18, 20 and 24 ms. Volumes for the amide 15 N- 1 H cross peaks were measured using NMRVIEW [17] and fitted with a single exponential decay function.…”

“…This small basic monomeric protein of 93 residues is structurally unrelated to other DNA-binding proteins [8], [9]. Its global fold consists of a pseudo barrel with an extension of the β-sheet ( β 4– β 5) forming an arm (LP5).…”